From d257744f6606616dba8c535bb1d72b4307e673b8 Mon Sep 17 00:00:00 2001 From: d4straub Date: Mon, 7 Jul 2025 19:24:25 +0200 Subject: [PATCH 1/5] add all nftest files --- .github/workflows/nf-test.yml | 2 +- tests/.nftignore | 20 +- tests/.nftignore_files_entirely | 5 + tests/default.nf.test | 4 +- tests/default.nf.test.snap | 1550 +----------------------- tests/dfast.nf.test | 36 + tests/dfast.nf.test.snap | 441 +++++++ tests/hybrid.nf.test | 36 + tests/hybrid.nf.test.snap | 480 ++++++++ tests/hybrid_dragonflye.nf.test | 36 + tests/hybrid_dragonflye.nf.test.snap | 471 +++++++ tests/long.nf.test | 36 + tests/long.nf.test.snap | 296 +++++ tests/long_dragonflye.nf.test | 36 + tests/long_dragonflye.nf.test.snap | 295 +++++ tests/long_liftoff.nf.test | 36 + tests/long_liftoff.nf.test.snap | 411 +++++++ tests/long_miniasm.nf.test | 36 + tests/long_miniasm.nf.test.snap | 382 ++++++ tests/long_miniasm_prokka.nf.test | 36 + tests/long_miniasm_prokka.nf.test.snap | 572 +++++++++ 21 files changed, 3659 insertions(+), 1558 deletions(-) create mode 100644 tests/.nftignore_files_entirely create mode 100644 tests/dfast.nf.test create mode 100644 tests/dfast.nf.test.snap create mode 100644 tests/hybrid.nf.test create mode 100644 tests/hybrid.nf.test.snap create mode 100644 tests/hybrid_dragonflye.nf.test create mode 100644 tests/hybrid_dragonflye.nf.test.snap create mode 100644 tests/long.nf.test create mode 100644 tests/long.nf.test.snap create mode 100644 tests/long_dragonflye.nf.test create mode 100644 tests/long_dragonflye.nf.test.snap create mode 100644 tests/long_liftoff.nf.test create mode 100644 tests/long_liftoff.nf.test.snap create mode 100644 tests/long_miniasm.nf.test create mode 100644 tests/long_miniasm.nf.test.snap create mode 100644 tests/long_miniasm_prokka.nf.test create mode 100644 tests/long_miniasm_prokka.nf.test.snap diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 325bc152..9bf9c59a 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -57,7 +57,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 7 + max_shards: 10 - name: debug run: | diff --git a/tests/.nftignore b/tests/.nftignore index be7bad20..70ba825d 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -8,23 +8,17 @@ multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html fastqc/*_fastqc.{html,zip} FastQC/raw/*.{html,zip} -FastQC/trim/*.html,zip +FastQC/trim/*.{html,zip} pipeline_info/*.{html,json,txt,yml} +busco/busco_downloads/** +busco/**/busco_sequences/** +busco/**/hmmer_output/** busco/*.batch_summary.txt -busco/*.log -busco/**/logs/hmmsearch_out.log -busco/**/.checkpoint -busco/**/hmmer_output/*.out -busco/**/run_bacteria_odb10/short_summary.{txt,json} +busco/**/*.{log,checkpoint} +busco/**/short_summary.*{txt,json} busco/*.batch_summary.txt -busco/short_summary.specific.bacteria_odb10.*.scaffolds.fa.{json,txt} trimming/shortreads/json_html/*.fastp.html trimming/shortreads/log/*.fastp.log Prokka/*/*.{gbk,sqn,log,err} -QUAST/report/basic_stats/*.scaffolds_GC_content_plot.pdf -QUAST/report/basic_stats/{GC_content_plot,Nx_plot,cumulative_plot}.pdf -QUAST/report/quast.log -QUAST/report/report.{html,pdf} +QUAST/report/** Unicycler/*.unicycler.log -.checkpoint -**/.checkpoint diff --git a/tests/.nftignore_files_entirely b/tests/.nftignore_files_entirely new file mode 100644 index 00000000..f60be8da --- /dev/null +++ b/tests/.nftignore_files_entirely @@ -0,0 +1,5 @@ +.DS_Store +pipeline_info/*.{html,json,txt} +busco/busco_downloads/** +busco/**/busco_sequences/** +busco/**/hmmer_output/** diff --git a/tests/default.nf.test b/tests/default.nf.test index c39fdc04..da489291 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -3,6 +3,8 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" tag "pipeline" + profile "test" + test("-profile test") { when { @@ -13,7 +15,7 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2756352e..7f96c3ea 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -130,382 +130,8 @@ "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/.bbtools_output", "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1009041at2.faa", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1009041at2.fna", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1024388at2.faa", - "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1024388at2.fna", - 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"1799923at2.hmm:md5,19b9d58d90669a7688a27851b12a9c6d", - "182107at2.hmm:md5,b9c4fa1879b93c2d74c5b83f221cf24c", - "1822215at2.hmm:md5,3dbf2959ecd80a285831bf1796bed24b", - "1822695at2.hmm:md5,c709dbe9ee7dd5481985043bd13bd5d8", - "1827295at2.hmm:md5,d59fe6c9f9cf3dda3e58c4921e0fcfce", - "1827334at2.hmm:md5,3d97cbe03c95af20605fc5c0c108e0f0", - "1830156at2.hmm:md5,bba0edf5f8f8efd837a2b4306f4869ef", - "1838961at2.hmm:md5,c8187444b548a4d1857b3751e0848515", - "1842956at2.hmm:md5,c8fdccf2bb98576201156067c9cb43bf", - "1844275at2.hmm:md5,1ab78432dff8bffab2efab7a92ce5308", - "1846503at2.hmm:md5,0dc9d03afee64cd70e094df338bbf5a8", - "1874945at2.hmm:md5,978e346758242e03e7c05b3ffec904f2", - "1890943at2.hmm:md5,4a9670ac0cfc1a1080f19d1d0481314d", - "1893906at2.hmm:md5,e87090b760ecfa89d053f3a7a3eb1541", - "1904463at2.hmm:md5,be2a02582773afe90720b261e3ae4462", - "1906715at2.hmm:md5,58f242511a6933207485cc0f0596e05c", - "1932144at2.hmm:md5,6eed45f2d0f5d623c39018ac0ff6e435", - "1937072at2.hmm:md5,370d311ee09b6474a3a6f65d72543902", - "1937493at2.hmm:md5,de435b0eedbaf3084ee97cb27075424f", - "1940575at2.hmm:md5,fbacbb9fc9066487b1bd3b2adb5e1b8f", - "1949059at2.hmm:md5,d1a05af40a15bad3e92830461ab59770", - "1959318at2.hmm:md5,8daf5eca17e062b1e4d2bfee5a1a0531", - "1963491at2.hmm:md5,b4d6a25ab961c538bd14bf3eccf68dac", - "1971380at2.hmm:md5,f80c4bab82dc353f244e7cba481d1948", - "1978865at2.hmm:md5,9c75295d2e839a2abaa3bc380f2e797b", - "1990141at2.hmm:md5,580641b551a56f89d68e5bb2adb27e60", - "1990650at2.hmm:md5,96f9126980ad497d97bb76e6644bfde9", - "2005443at2.hmm:md5,1013f2177a4572e5674b9d4e9c3b822b", - "2012682at2.hmm:md5,755fcb8353ec4a43ca14ad3785e5a03a", - "2035880at2.hmm:md5,b8b4392c8db05c496d6a227601396a3e", - "2040741at2.hmm:md5,332ee1d089c0b60c9b48306734d5de10", - "2046660at2.hmm:md5,b2b302c3f0e5a15d2d60a56b288bb917", - "2063644at2.hmm:md5,94ccc7d917810cee156fdcc1c75ea7d1", - "2066663at2.hmm:md5,522af87a80ec8ac36a8e4c142e9a29eb", - "2075502at2.hmm:md5,8461a52fd2de7548804b69f61fcb84ce", - "219876at2.hmm:md5,7f5d1813517c5fe910766501a1fb4f1c", - "223233at2.hmm:md5,219ae3102610d3d980fabd42af33a89d", - "226836at2.hmm:md5,7d12206040c7608c6528e86ab9f3f1f4", - "232152at2.hmm:md5,4aa760349b402b04d06908a0f35bf475", - "26038at2.hmm:md5,c8f0e5fdd2489863a4d5505bdde96d39", - "267682at2.hmm:md5,353899e4cabc82ace16efc7e6f07dc90", - "353391at2.hmm:md5,b4efae4ca10321b1e94dba4b2f374d70", - "384865at2.hmm:md5,05a169cbcb7dce7627af9fcc80335b0a", - "402899at2.hmm:md5,ed29359bea9213c400f63f2fd1613255", - "430176at2.hmm:md5,4b3774c425104112739cee46e7f9d615", - "4421at2.hmm:md5,7a48f6f002fce2058ef7e46013a0752a", - "462069at2.hmm:md5,67618eea22d5b8f51b2a1aebcc9c26bd", - "469058at2.hmm:md5,f89dfc63758a2fd8f6f19fdab0f1f491", - "504464at2.hmm:md5,11d0689354ac6ed159137d54217d6218", - "505485at2.hmm:md5,8de48fd1871731f37e64693a37edb982", - "533698at2.hmm:md5,69b2f806959b50a68efc7176c12d74bf", - "662686at2.hmm:md5,5185b790632cc569935d5be75e30fefb", - "665824at2.hmm:md5,acdcc74bc2849a80bb17b982868ebfe1", - "761140at2.hmm:md5,7cee7ca9098bee73f284012f6e9882eb", - "776861at2.hmm:md5,b0674fc40b4abb60a0cb4c4638d3f3f3", - "837522at2.hmm:md5,b14e6d3ce456b6153d31b56c273851c9", - "841869at2.hmm:md5,853efdc34974d4a8e1bb54a67dedafdc", - "874197at2.hmm:md5,3e205a7bd43377ee447ae4a37aa3e881", - "91428at2.hmm:md5,74464fecdfc8ebb5741ae7b58b226230", - "923547at2.hmm:md5,1bf19a58d6470f775802f263ff6621ba", - "932854at2.hmm:md5,01122df842330c8db68752689f0fbdb1", - "932993at2.hmm:md5,787d887ffd8a11531bd3c6216d032201", - "95696at2.hmm:md5,5025fe62fd6327ad77736087d12a98f2", - "9601at2.hmm:md5,95410183ed2c3faca0b164186a1b8026", - "961486at2.hmm:md5,3b268f8c45dfaa31eb0cb22477d73c1c", - "981870at2.hmm:md5,b1df3ac0dd764bb6e0e49a5dbf7c798d", - "984717at2.hmm:md5,489e218d52d2d0b47b8042820ee11ac6", - "ogs.id.info:md5,1ca22225d2f86e6e633e1a1a204d9a3a", - "species.info:md5,ce4c2ce47d3d8503bda2a1c2866430ff", - "lengths_cutoff:md5,19e7d86a63987906c6c6e6861f7526d0", - "links_to_ODB10.txt:md5,4c2d02208a8cb03980853823ae8803cb", - "refseq_db.faa.gz:md5,b0dd2e4f367d4fe194c3df3af5eae440", - "refseq_db.faa.gz.md5:md5,7c4129b91e9ecb1aa3286d1293fa29ea", - "scores_cutoff:md5,6c6fb593a83d5da8b2909d70a4f15df9", + "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.json:md5,34cdcc175fec96077a9939f3cb82c362", + "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.txt:md5,d2e0ca4b1d89cce2f99a538a7384ea3b", + "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.json:md5,7d29e4d61a7b04c81afcc8581fc81cef", + "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.txt:md5,b17547d30049b5e626d3463a32e46190", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,2e1c897d672181a4ee893911dc23b679", "mqc_fastp-insert-size-plot_1.yaml:md5,1da35415f0542ec3d3f6d6d7d250ae32", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,23ace34b503b638ef667647f7de2020a", @@ -1978,6 +442,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-01T16:33:24.372012843" + "timestamp": "2025-07-07T17:47:19.529150043" } } \ No newline at end of file diff --git a/tests/dfast.nf.test b/tests/dfast.nf.test new file mode 100644 index 00000000..75648052 --- /dev/null +++ b/tests/dfast.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_dfast" + + test("-profile test_dfast") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/dfast.nf.test.snap b/tests/dfast.nf.test.snap new file mode 100644 index 00000000..d85fc8b9 --- /dev/null +++ b/tests/dfast.nf.test.snap @@ -0,0 +1,441 @@ +{ + "-profile test_dfast": { + "content": [ + 14, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "DFAST": { + "dfast": "1.3.2" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "FASTQC_RAW": { + "fastqc": "0.12.1" + }, + "FASTQC_TRIM": { + "fastqc": "0.12.1" + }, + "QUAST": { + "quast": "5.2.0" + }, + "UNICYCLER": { + "unicycler": "0.5.0" + }, + "Workflow": { + "nf-core/bacass": "v2.5.0dev" + } + }, + [ + "DFAST", + "DFAST/ERR044595_results", + "DFAST/ERR044595_results/application.log", + "DFAST/ERR044595_results/cds.fna", + "DFAST/ERR044595_results/ddbj", + "DFAST/ERR044595_results/ddbj/mss.ann", + "DFAST/ERR044595_results/ddbj/mss.fasta", + "DFAST/ERR044595_results/genome.embl", + "DFAST/ERR044595_results/genome.fna", + "DFAST/ERR044595_results/genome.gbk", + "DFAST/ERR044595_results/genome.gff", + "DFAST/ERR044595_results/protein.faa", + "DFAST/ERR044595_results/pseudogene_summary.tsv", + "DFAST/ERR044595_results/rna.fna", + "DFAST/ERR044595_results/statistics.txt", + "DFAST/ERR064912_results", + "DFAST/ERR064912_results/application.log", + "DFAST/ERR064912_results/cds.fna", + "DFAST/ERR064912_results/ddbj", + "DFAST/ERR064912_results/ddbj/mss.ann", + "DFAST/ERR064912_results/ddbj/mss.fasta", + "DFAST/ERR064912_results/genome.embl", + "DFAST/ERR064912_results/genome.fna", + "DFAST/ERR064912_results/genome.gbk", + "DFAST/ERR064912_results/genome.gff", + "DFAST/ERR064912_results/protein.faa", + "DFAST/ERR064912_results/pseudogene_summary.tsv", + "DFAST/ERR064912_results/rna.fna", + "DFAST/ERR064912_results/statistics.txt", + "FastQC", + "FastQC/raw", + "FastQC/raw/ERR044595_1_fastqc.html", + "FastQC/raw/ERR044595_1_fastqc.zip", + "FastQC/raw/ERR044595_2_fastqc.html", + "FastQC/raw/ERR044595_2_fastqc.zip", + "FastQC/raw/ERR064912_1_fastqc.html", + "FastQC/raw/ERR064912_1_fastqc.zip", + "FastQC/raw/ERR064912_2_fastqc.html", + "FastQC/raw/ERR064912_2_fastqc.zip", + "FastQC/trim", + "FastQC/trim/ERR044595_1_fastqc.html", + "FastQC/trim/ERR044595_2_fastqc.html", + "FastQC/trim/ERR064912_1_fastqc.html", + "FastQC/trim/ERR064912_2_fastqc.html", + "QUAST", + "QUAST/report", + "QUAST/report/basic_stats", + "QUAST/report/basic_stats/ERR044595.scaffolds_GC_content_plot.pdf", + "QUAST/report/basic_stats/ERR064912.scaffolds_GC_content_plot.pdf", + "QUAST/report/basic_stats/GC_content_plot.pdf", + "QUAST/report/basic_stats/Nx_plot.pdf", + "QUAST/report/basic_stats/cumulative_plot.pdf", + "QUAST/report/icarus.html", + "QUAST/report/icarus_viewers", + "QUAST/report/icarus_viewers/contig_size_viewer.html", + "QUAST/report/quast.log", + "QUAST/report/report.html", + "QUAST/report/report.pdf", + "QUAST/report/report.tex", + "QUAST/report/report.tsv", + "QUAST/report/report.txt", + "QUAST/report/transposed_report.tex", + "QUAST/report/transposed_report.tsv", + "QUAST/report/transposed_report.txt", + "Unicycler", + "Unicycler/ERR044595.assembly.gfa.gz", + "Unicycler/ERR044595.scaffolds.fa.gz", + "Unicycler/ERR044595.unicycler.log", + "Unicycler/ERR064912.assembly.gfa.gz", + "Unicycler/ERR064912.scaffolds.fa.gz", + "Unicycler/ERR064912.unicycler.log", + "busco", + "busco/ERR044595-bacteria_odb10-busco", + "busco/ERR044595-bacteria_odb10-busco.batch_summary.txt", + "busco/ERR044595-bacteria_odb10-busco.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs/bbtools_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs/bbtools_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs/hmmsearch_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs/hmmsearch_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs/prodigal_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/logs/prodigal_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/.checkpoint", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/predicted.faa", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/predicted.fna", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/tmp", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/.bbtools_output", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/busco_sequences", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/full_table.tsv", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/hmmer_output", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/missing_busco_list.tsv", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/short_summary.json", + "busco/ERR044595-bacteria_odb10-busco/ERR044595.scaffolds.fa/run_bacteria_odb10/short_summary.txt", + "busco/ERR044595-bacteria_odb10-busco/logs", + "busco/ERR064912-bacteria_odb10-busco", + "busco/ERR064912-bacteria_odb10-busco.batch_summary.txt", + "busco/ERR064912-bacteria_odb10-busco.log", + "busco/ERR064912-bacteria_odb10-busco/ERR064912.scaffolds.fa", + 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"mqc_fastp-seq-quality-plot_Read_1_After_filtering.yaml:md5,b6d62af1e24d74cfc8860e2c3bb1e1f8", + "mqc_fastp-seq-quality-plot_Read_1_Before_filtering.yaml:md5,8a2f99badd4307372fbf3cbad6d0ea1d", + "mqc_fastp-seq-quality-plot_Read_2_After_filtering.yaml:md5,b6cd211a33c6a5ea2f33ba0b8bff2e12", + "mqc_fastp-seq-quality-plot_Read_2_Before_filtering.yaml:md5,53b11895fa7b0f3a217c6d08b656edde", + "mqc_fastp_filtered_reads_plot_1.yaml:md5,8b8ca8b9b2ba74ff4878848ccc7a0c1f", + "mqc_fastqc_adapter_content_plot_1.yaml:md5,03765b759de8ca659af65aa226a0c91b", + "mqc_fastqc_per_base_n_content_plot-2_1.yaml:md5,133136f55a621314f29395b0b590e02c", + "mqc_fastqc_per_base_n_content_plot_1.yaml:md5,7c8cebddb77c63cf63e31c559c02c9fa", + "mqc_fastqc_per_base_sequence_quality_plot-2_1.yaml:md5,c36608746f280013ed31fe1d3b6059de", + "mqc_fastqc_per_base_sequence_quality_plot_1.yaml:md5,8b543fd862b00615123e5a62be0d5099", + "mqc_fastqc_per_sequence_gc_content_plot-2_Counts.yaml:md5,a9e7955b572fcb86414dd273c648141f", + "mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.yaml:md5,ec175b43fc74064aac53695244cd47d7", + "mqc_fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,786db52131724d97f598f14b17e15e1c", + "mqc_fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,569ff6b6eee59b26ce354b4b93f2fdc4", + "mqc_fastqc_per_sequence_quality_scores_plot-2_1.yaml:md5,6a83696e544a9d39db9231efc91915ad", + "mqc_fastqc_per_sequence_quality_scores_plot_1.yaml:md5,e9012a938a3e11c0bd9847d18273fe88", + "mqc_fastqc_sequence_counts_plot-2_1.yaml:md5,9c4bf16973d87cfe3731b660fffb4ddb", + "mqc_fastqc_sequence_counts_plot_1.yaml:md5,a940e04693bcbadf20405148a1b1be35", + "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,904ae9ce7abc638239879b6d16ff80a8", + "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,4839cd6c3bd11763f6f58ec0c1fd75b2", + "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,2a0bfc0ec257081a52bf4f1755dd246b", + "mqc_quast_num_contigs_1.yaml:md5,98c3bbef635dac3f5afe78c1f6718e5e", + "multiqc_busco.yaml:md5,003b890081970ec29305149c67f67cc9", + "multiqc_citations.yaml:md5,e46f6ed003947fe967edd4674a82d4c6", + "multiqc_fastp.yaml:md5,562cb7689bb8074a7bca26ae8a129996", + "multiqc_fastqc.yaml:md5,05172556a25feb1277e789e91031d3bc", + "multiqc_fastqc_1.yaml:md5,a4bc353bd4a67c1f480fb890d806bf6a", + "multiqc_general_stats.yaml:md5,c1a9086493cf9a79e03a29941dbddd85", + "multiqc_quast.yaml:md5,b6d3146c4a0fdf49d430d6df87cf2577", + "ERR044595.fastp.json:md5,ab69a1d8f62b6e1be76c83bb1022e882", + "ERR064912.fastp.json:md5,b79afd61a88a0637d49b78537c2938e8" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.2" + }, + "timestamp": "2025-07-07T18:12:16.674942373" + } +} \ No newline at end of file diff --git a/tests/hybrid.nf.test b/tests/hybrid.nf.test new file mode 100644 index 00000000..bf98981a --- /dev/null +++ b/tests/hybrid.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_hybrid" + + test("-profile test_hybrid") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/hybrid.nf.test.snap b/tests/hybrid.nf.test.snap new file mode 100644 index 00000000..013293bb --- /dev/null +++ b/tests/hybrid.nf.test.snap @@ -0,0 +1,480 @@ +{ + "-profile test_hybrid": { + "content": [ + 12, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "FASTQC_RAW": { + "fastqc": "0.12.1" + }, + "FASTQC_TRIM": { + "fastqc": "0.12.1" + }, + "MEDAKA": { + "medaka": "1.4.3" + }, + "NANOPLOT": { + "nanoplot": "1.41.6" + }, + "PORECHOP_PORECHOP": { + "porechop": "0.2.4" + }, + "PROKKA": { + "prokka": "1.14.6" + }, + "QUAST": { + "quast": "5.2.0" + }, + "TOULLIGQC": { + "toulligqc": "2.5.6" + }, + "UNICYCLER": { + "unicycler": "0.5.0" + }, + "Workflow": { + "nf-core/bacass": "v2.5.0dev" + } + }, + [ + "FastQC", + "FastQC/raw", + "FastQC/raw/ERR044595_1_fastqc.html", + "FastQC/raw/ERR044595_1_fastqc.zip", + "FastQC/raw/ERR044595_2_fastqc.html", + "FastQC/raw/ERR044595_2_fastqc.zip", + "FastQC/trim", + "FastQC/trim/ERR044595_1_fastqc.html", + "FastQC/trim/ERR044595_2_fastqc.html", + "Medaka", + "Medaka/ERR044595_polished_genome.fa", + "Prokka", + "Prokka/ERR044595", + "Prokka/ERR044595/ERR044595.err", + "Prokka/ERR044595/ERR044595.faa", + "Prokka/ERR044595/ERR044595.ffn", + "Prokka/ERR044595/ERR044595.fna", + "Prokka/ERR044595/ERR044595.fsa", + "Prokka/ERR044595/ERR044595.gbk", + "Prokka/ERR044595/ERR044595.gff", + "Prokka/ERR044595/ERR044595.log", + "Prokka/ERR044595/ERR044595.sqn", + "Prokka/ERR044595/ERR044595.tbl", + "Prokka/ERR044595/ERR044595.tsv", + "Prokka/ERR044595/ERR044595.txt", + "QC_longreads", + "QC_longreads/NanoPlot", + "QC_longreads/NanoPlot/ERR044595.txt", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.png", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", + "QC_longreads/NanoPlot/NanoPlot-report.html", + "QC_longreads/NanoPlot/NanoPlot_20250707_1812.log", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.png", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/Yield_By_Length.html", + "QC_longreads/NanoPlot/Yield_By_Length.png", + "QC_longreads/ToulligQC", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Channel_occupancy_of_the_flowcell.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Correlation_between_read_length_and_PHRED_score.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Distribution_of_read_lengths.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/PHRED_score_density_distribution.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/PHRED_score_distribution.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/PHRED_score_over_time.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Read_count_histogram.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Read_length_over_time.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Yield_plot_through_time.html", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/plotly.min.js", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/report.data", + "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/report.html", + "QUAST", + "QUAST/report", + "QUAST/report/basic_stats", + "QUAST/report/basic_stats/ERR044595_polished_genome_GC_content_plot.pdf", + "QUAST/report/basic_stats/GC_content_plot.pdf", + "QUAST/report/basic_stats/Nx_plot.pdf", + "QUAST/report/basic_stats/cumulative_plot.pdf", + "QUAST/report/icarus.html", + "QUAST/report/icarus_viewers", + "QUAST/report/icarus_viewers/contig_size_viewer.html", + "QUAST/report/quast.log", + "QUAST/report/report.html", + "QUAST/report/report.pdf", + "QUAST/report/report.tex", + "QUAST/report/report.tsv", + "QUAST/report/report.txt", + "QUAST/report/transposed_report.tex", + "QUAST/report/transposed_report.tsv", + "QUAST/report/transposed_report.txt", + "Unicycler", + "Unicycler/ERR044595.assembly.gfa.gz", + "Unicycler/ERR044595.scaffolds.fa.gz", + "Unicycler/ERR044595.unicycler.log", + "busco", + "busco/ERR044595-bacteria_odb10-busco", + "busco/ERR044595-bacteria_odb10-busco.batch_summary.txt", + "busco/ERR044595-bacteria_odb10-busco.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs/bbtools_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs/bbtools_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs/hmmsearch_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs/hmmsearch_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs/prodigal_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/logs/prodigal_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/.checkpoint", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/predicted.faa", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/predicted.fna", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/tmp", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/.bbtools_output", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/busco_sequences", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/full_table.tsv", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/hmmer_output", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/missing_busco_list.tsv", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/short_summary.json", + "busco/ERR044595-bacteria_odb10-busco/ERR044595_polished_genome.fa/run_bacteria_odb10/short_summary.txt", + "busco/ERR044595-bacteria_odb10-busco/logs", + "busco/busco_downloads", + "busco/short_summary.specific.bacteria_odb10.ERR044595_polished_genome.fa.json", + "busco/short_summary.specific.bacteria_odb10.ERR044595_polished_genome.fa.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/mqc_busco_plot_bacteria_odb10_1.yaml", + "multiqc/multiqc_data/mqc_fastp-insert-size-plot_1.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_1_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_2_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_2_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_1_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_1_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_2_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_2_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_1_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_1_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_2_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_2_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp_filtered_reads_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_adapter_content_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_n_content_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot-2_Counts.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_sequence_counts_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_sequence_counts_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_sequence_length_distribution_plot_1.yaml", + "multiqc/multiqc_data/mqc_nanostat_quality_dist_1.yaml", + "multiqc/multiqc_data/mqc_porechop-endtrim-barplot_1.yaml", + 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"mqc_fastqc_per_base_n_content_plot_1.yaml:md5,487a503d88d3f528efbd4b31370be212", + "mqc_fastqc_per_base_sequence_quality_plot-2_1.yaml:md5,d64472aafb8e6ab2adcf9081c1f40bf5", + "mqc_fastqc_per_base_sequence_quality_plot_1.yaml:md5,998d5867246dc727d4b2ff0f6114976a", + "mqc_fastqc_per_sequence_gc_content_plot-2_Counts.yaml:md5,929297caab6aaab9391f1f04134e34ac", + "mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.yaml:md5,d344d907c13477bf254257ed575aea4e", + "mqc_fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,629e47dd842b85da55155049f57245ed", + "mqc_fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,ab88d368ab782e2d54700986418d8eed", + "mqc_fastqc_per_sequence_quality_scores_plot-2_1.yaml:md5,c27ccef7d4d47bda512004aa471e7e0a", + "mqc_fastqc_per_sequence_quality_scores_plot_1.yaml:md5,9c94c30d8c79c371a0ee23e5f7464298", + "mqc_fastqc_sequence_counts_plot-2_1.yaml:md5,f9bf9a0442ea4597a3d921a556dad0e5", + "mqc_fastqc_sequence_counts_plot_1.yaml:md5,2016ce12f38f1c0055896a97c239e8e8", + "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,40b02d3d1c520ab503db1bb0e8e0caa1", + "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,6d48bc221cdbc5943d4723d3f57cdd1e", + "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,09590048b87067b8d7d3495f44d7795d", + "mqc_nanostat_quality_dist_1.yaml:md5,38867760d093f7b04abb5e03e748573a", + "mqc_porechop-endtrim-barplot_1.yaml:md5,29573e9fc6174bb91352b0b9f248335f", + "mqc_porechop-middlesplit-barplot_1.yaml:md5,844b018c7434ca59c893901eef530de8", + "mqc_porechop-starttrim-barplot_1.yaml:md5,e6cced8fc844dabd795ba0dfa6ec0e64", + "mqc_prokka_plot_1.yaml:md5,4033ae78aa4b6e61b2b2925ab4122b80", + "mqc_quast_num_contigs_1.yaml:md5,fb56467c2cc7e7dfd50d6d306c7defd9", + "multiqc_busco.yaml:md5,cc14257553d13289016474578391216c", + "multiqc_citations.yaml:md5,c1962a840fe1cf1698fbdeb8953601ed", + "multiqc_fastp.yaml:md5,c77f208bad399ef0250ae293a9d35a4e", + "multiqc_fastqc.yaml:md5,68dcba3602303c17700845789c5228fb", + "multiqc_fastqc_1.yaml:md5,9e5474735bdcccbaf6f2bd6039b1a4ee", + "multiqc_general_stats.yaml:md5,03cbcdcfa7fb04eab2640c7f54831b7e", + "multiqc_nanostat.yaml:md5,b15cabc45adc271cd6d355ec18244ddc", + "multiqc_prokka.yaml:md5,8f1bc1653918ac57728dd2eb107615da", + "multiqc_quast.yaml:md5,b32bf4c828a4e8b5c6a6d1e51a700158", + "porechop.yaml:md5,7c5b60ab31a49def692703989e225413", + "ERR044595.porechop.log:md5,60d5a94c87e738472e0f9415fd89d8e8", + "ERR044595.fastp.json:md5,ab69a1d8f62b6e1be76c83bb1022e882" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.2" + }, + "timestamp": "2025-07-07T18:24:31.096595535" + } +} \ No newline at end of file diff --git a/tests/hybrid_dragonflye.nf.test b/tests/hybrid_dragonflye.nf.test new file mode 100644 index 00000000..fe2455b4 --- /dev/null +++ b/tests/hybrid_dragonflye.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_hybrid_dragonflye" + + test("-profile test_hybrid_dragonflye") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/hybrid_dragonflye.nf.test.snap b/tests/hybrid_dragonflye.nf.test.snap new file mode 100644 index 00000000..9fc5dd0b --- /dev/null +++ b/tests/hybrid_dragonflye.nf.test.snap @@ -0,0 +1,471 @@ +{ + "-profile test_hybrid_dragonflye": { + "content": [ + 12, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "DRAGONFLYE": { + "dragonflye": "1.1.2" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "FASTQC_RAW": { + "fastqc": "0.12.1" + }, + "FASTQC_TRIM": { + "fastqc": "0.12.1" + }, + "MEDAKA": { + "medaka": "1.4.3" + }, + "NANOPLOT": { + "nanoplot": "1.41.6" + }, + "PORECHOP_PORECHOP": { + "porechop": "0.2.4" + }, + "PROKKA": { + "prokka": "1.14.6" + }, + "QUAST": { + "quast": "5.2.0" + }, + "TOULLIGQC": { + "toulligqc": "2.5.6" + }, + "Workflow": { + "nf-core/bacass": "v2.5.0dev" + } + }, + [ + "Dragonflye", + "Dragonflye/A1403KPN.dragonflye.log", + "Dragonflye/A1403KPN.fa", + "FastQC", + "FastQC/raw", + "FastQC/raw/A1403KPN_1_fastqc.html", + "FastQC/raw/A1403KPN_1_fastqc.zip", + "FastQC/raw/A1403KPN_2_fastqc.html", + "FastQC/raw/A1403KPN_2_fastqc.zip", + "FastQC/trim", + "FastQC/trim/A1403KPN_1_fastqc.html", + "FastQC/trim/A1403KPN_2_fastqc.html", + "Medaka", + "Medaka/A1403KPN_polished_genome.fa", + "Prokka", + "Prokka/A1403KPN", + "Prokka/A1403KPN/A1403KPN.err", + "Prokka/A1403KPN/A1403KPN.faa", + "Prokka/A1403KPN/A1403KPN.ffn", + "Prokka/A1403KPN/A1403KPN.fna", + "Prokka/A1403KPN/A1403KPN.fsa", + "Prokka/A1403KPN/A1403KPN.gbk", + "Prokka/A1403KPN/A1403KPN.gff", + "Prokka/A1403KPN/A1403KPN.log", + "Prokka/A1403KPN/A1403KPN.sqn", + "Prokka/A1403KPN/A1403KPN.tbl", + "Prokka/A1403KPN/A1403KPN.tsv", + "Prokka/A1403KPN/A1403KPN.txt", + "QC_longreads", + "QC_longreads/NanoPlot", + "QC_longreads/NanoPlot/A1403KPN.txt", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.png", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", + "QC_longreads/NanoPlot/NanoPlot-report.html", + "QC_longreads/NanoPlot/NanoPlot_20250707_1825.log", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.png", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/Yield_By_Length.html", + "QC_longreads/NanoPlot/Yield_By_Length.png", + "QC_longreads/ToulligQC", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/Correlation_between_read_length_and_PHRED_score.html", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/Distribution_of_read_lengths.html", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/PHRED_score_density_distribution.html", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/PHRED_score_distribution.html", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/Read_count_histogram.html", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/plotly.min.js", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/report.data", + "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/report.html", + "QUAST", + "QUAST/report", + "QUAST/report/basic_stats", + "QUAST/report/basic_stats/A1403KPN_polished_genome_GC_content_plot.pdf", + "QUAST/report/basic_stats/GC_content_plot.pdf", + "QUAST/report/basic_stats/Nx_plot.pdf", + "QUAST/report/basic_stats/cumulative_plot.pdf", + "QUAST/report/icarus.html", + "QUAST/report/icarus_viewers", + "QUAST/report/icarus_viewers/contig_size_viewer.html", + "QUAST/report/quast.log", + "QUAST/report/report.html", + "QUAST/report/report.pdf", + "QUAST/report/report.tex", + "QUAST/report/report.tsv", + "QUAST/report/report.txt", + "QUAST/report/transposed_report.tex", + "QUAST/report/transposed_report.tsv", + "QUAST/report/transposed_report.txt", + "busco", + "busco/A1403KPN-bacteria_odb10-busco", + "busco/A1403KPN-bacteria_odb10-busco.batch_summary.txt", + "busco/A1403KPN-bacteria_odb10-busco.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs/bbtools_err.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs/bbtools_out.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs/hmmsearch_err.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs/hmmsearch_out.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs/prodigal_err.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/logs/prodigal_out.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/.checkpoint", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/predicted.faa", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/predicted.fna", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/tmp", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/.bbtools_output", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/busco_sequences", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/full_table.tsv", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/hmmer_output", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/missing_busco_list.tsv", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/short_summary.json", + "busco/A1403KPN-bacteria_odb10-busco/A1403KPN_polished_genome.fa/run_bacteria_odb10/short_summary.txt", + "busco/A1403KPN-bacteria_odb10-busco/logs", + "busco/busco_downloads", + "busco/short_summary.specific.bacteria_odb10.A1403KPN_polished_genome.fa.json", + "busco/short_summary.specific.bacteria_odb10.A1403KPN_polished_genome.fa.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/mqc_busco_plot_bacteria_odb10_1.yaml", + "multiqc/multiqc_data/mqc_fastp-insert-size-plot_1.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_1_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_2_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-gc-plot_Read_2_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_1_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_1_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_2_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-content-n-plot_Read_2_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_1_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_1_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_2_After_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp-seq-quality-plot_Read_2_Before_filtering.yaml", + "multiqc/multiqc_data/mqc_fastp_filtered_reads_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_n_content_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot-2_Counts.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot-2_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.yaml", + "multiqc/multiqc_data/mqc_fastqc_sequence_counts_plot-2_1.yaml", + 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"mqc_fastqc_per_base_n_content_plot_1.yaml:md5,58e25858251be700167d277c356de29f", + "mqc_fastqc_per_base_sequence_quality_plot-2_1.yaml:md5,92c672625e8cc282f043b406574fdee7", + "mqc_fastqc_per_base_sequence_quality_plot_1.yaml:md5,a4bdafea78e4a1049e4e6ce2b1a7e816", + "mqc_fastqc_per_sequence_gc_content_plot-2_Counts.yaml:md5,bc9cc5b8db8da387bab8e46fe29ec9f0", + "mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.yaml:md5,7b9461bb648346514d1dde264cab0ce9", + "mqc_fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,51925369c6520f704450148fd9547fc7", + "mqc_fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,3c573781c5d682cdc8680e5d092e4745", + "mqc_fastqc_per_sequence_quality_scores_plot-2_1.yaml:md5,a7e42c87513455a805052fecde398534", + "mqc_fastqc_per_sequence_quality_scores_plot_1.yaml:md5,f74d59e6e31ce5a08526df2478e89e82", + "mqc_fastqc_sequence_counts_plot-2_1.yaml:md5,048f6e23e07442e79aed309bd8209cd7", + "mqc_fastqc_sequence_counts_plot_1.yaml:md5,92ddea214b555d616986db63a27c2fd8", + "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,5a54bfac7a3c5f58437aea95367ea1a9", + "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,48bcfc30b81a4a77fca5ff31b97a1b94", + "mqc_fastqc_sequence_length_distribution_plot-2_1.yaml:md5,d13a473647db97788ee55c40278e8884", + "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,b61ee98db5dbee6c5e74e7e77567f9c2", + "mqc_nanostat_quality_dist_1.yaml:md5,e9b3d36de04919a03bde805a3e2df7a1", + "mqc_porechop-endtrim-barplot_1.yaml:md5,a6396edf17f4e4ed9954cda933af2b7b", + "mqc_porechop-middlesplit-barplot_1.yaml:md5,5e89ca1f45fb6876b58ddbb20b86ea77", + "mqc_porechop-starttrim-barplot_1.yaml:md5,34e8d91183bd582532ac654e8e287945", + "mqc_prokka_plot_1.yaml:md5,263db317035745f5925103b1c09883cb", + "mqc_quast_num_contigs_1.yaml:md5,ddacf823d2fd44a8d39d62b3d8b36a06", + "multiqc_busco.yaml:md5,b645040c8295ca4a3b63af126dc68633", + "multiqc_citations.yaml:md5,c1962a840fe1cf1698fbdeb8953601ed", + "multiqc_fastp.yaml:md5,ed975e259ac4db3e9c2ba4dcd618fc18", + "multiqc_fastqc.yaml:md5,a0b5fd24bb745bb77511c1962086fcf0", + "multiqc_fastqc_1.yaml:md5,daf5f34bdacbbc207f86fc95768ce9a2", + "multiqc_general_stats.yaml:md5,91adec7ffafa3963479c557acde9245f", + "multiqc_nanostat.yaml:md5,c9346968eeb2741d12322c9a5bb0c6c2", + "multiqc_prokka.yaml:md5,96845fe8945572f8a7df13228f75ba9b", + "multiqc_quast.yaml:md5,145f1ceae2b16c1e86d73d8ee7e44b87", + "porechop.yaml:md5,eee3e2eb251a026d42d70720da49fb4d", + "A1403KPN.porechop.log:md5,552282af03b80736e49b39466e9ba4b5", + "A1403KPN.fastp.json:md5,be3cb43a0cfe3d2bd4990953318262d2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.2" + }, + "timestamp": "2025-07-07T18:39:53.525898974" + } +} \ No newline at end of file diff --git a/tests/long.nf.test b/tests/long.nf.test new file mode 100644 index 00000000..3f762164 --- /dev/null +++ b/tests/long.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_long" + + test("-profile test_long") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/long.nf.test.snap b/tests/long.nf.test.snap new file mode 100644 index 00000000..0ea564e5 --- /dev/null +++ b/tests/long.nf.test.snap @@ -0,0 +1,296 @@ +{ + "-profile test_long": { + "content": [ + 9, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "MEDAKA": { + "medaka": "1.4.3" + }, + "NANOPLOT": { + "nanoplot": "1.41.6" + }, + "PORECHOP_PORECHOP": { + "porechop": "0.2.4" + }, + "PROKKA": { + "prokka": "1.14.6" + }, + "QUAST": { + "quast": "5.2.0" + }, + "TOULLIGQC": { + "toulligqc": "2.5.6" + }, + "UNICYCLER": { + "unicycler": "0.5.0" + }, + "Workflow": { + "nf-core/bacass": "v2.5.0dev" + } + }, + [ + "Medaka", + "Medaka/TestMe_polished_genome.fa", + "Prokka", + "Prokka/TestMe", + "Prokka/TestMe/TestMe.err", + "Prokka/TestMe/TestMe.faa", + "Prokka/TestMe/TestMe.ffn", + "Prokka/TestMe/TestMe.fna", + "Prokka/TestMe/TestMe.fsa", + "Prokka/TestMe/TestMe.gbk", + "Prokka/TestMe/TestMe.gff", + "Prokka/TestMe/TestMe.log", + "Prokka/TestMe/TestMe.sqn", + "Prokka/TestMe/TestMe.tbl", + "Prokka/TestMe/TestMe.tsv", + "Prokka/TestMe/TestMe.txt", + "QC_longreads", + "QC_longreads/NanoPlot", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.png", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", + "QC_longreads/NanoPlot/NanoPlot-report.html", + "QC_longreads/NanoPlot/NanoPlot_20250707_1840.log", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/TestMe.txt", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.png", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/Yield_By_Length.html", + "QC_longreads/NanoPlot/Yield_By_Length.png", + "QC_longreads/ToulligQC", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Channel_occupancy_of_the_flowcell.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Correlation_between_read_length_and_PHRED_score.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Distribution_of_read_lengths.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/PHRED_score_density_distribution.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/PHRED_score_distribution.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/PHRED_score_over_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Read_count_histogram.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Read_length_over_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Yield_plot_through_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/plotly.min.js", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/report.data", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/report.html", + "QUAST", + "QUAST/report", + "QUAST/report/basic_stats", + "QUAST/report/basic_stats/GC_content_plot.pdf", + "QUAST/report/basic_stats/Nx_plot.pdf", + "QUAST/report/basic_stats/TestMe_polished_genome_GC_content_plot.pdf", + "QUAST/report/basic_stats/cumulative_plot.pdf", + "QUAST/report/icarus.html", + "QUAST/report/icarus_viewers", + "QUAST/report/icarus_viewers/contig_size_viewer.html", + "QUAST/report/quast.log", + "QUAST/report/report.html", + "QUAST/report/report.pdf", + "QUAST/report/report.tex", + "QUAST/report/report.tsv", + "QUAST/report/report.txt", + "QUAST/report/transposed_report.tex", + "QUAST/report/transposed_report.tsv", + "QUAST/report/transposed_report.txt", + "Unicycler", + "Unicycler/TestMe.assembly.gfa.gz", + "Unicycler/TestMe.scaffolds.fa.gz", + "Unicycler/TestMe.unicycler.log", + "busco", + "busco/TestMe-bacteria_odb10-busco", + "busco/TestMe-bacteria_odb10-busco.batch_summary.txt", + "busco/TestMe-bacteria_odb10-busco.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/bbtools_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/bbtools_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/hmmsearch_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/hmmsearch_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/prodigal_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/prodigal_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/.checkpoint", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/predicted.faa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/predicted.fna", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.faa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4.fna", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_4_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/.bbtools_output", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/full_table.tsv", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/missing_busco_list.tsv", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/short_summary.json", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/short_summary.txt", + "busco/TestMe-bacteria_odb10-busco/logs", + "busco/busco_downloads", + "busco/short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json", + "busco/short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/mqc_busco_plot_bacteria_odb10_1.yaml", + "multiqc/multiqc_data/mqc_nanostat_quality_dist_1.yaml", + "multiqc/multiqc_data/mqc_porechop-endtrim-barplot_1.yaml", + "multiqc/multiqc_data/mqc_porechop-middlesplit-barplot_1.yaml", + "multiqc/multiqc_data/mqc_porechop-starttrim-barplot_1.yaml", + "multiqc/multiqc_data/mqc_prokka_plot_1.yaml", + "multiqc/multiqc_data/mqc_quast_num_contigs_1.yaml", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_busco.yaml", + "multiqc/multiqc_data/multiqc_citations.yaml", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.yaml", + "multiqc/multiqc_data/multiqc_nanostat.yaml", + "multiqc/multiqc_data/multiqc_prokka.yaml", + "multiqc/multiqc_data/multiqc_quast.yaml", + "multiqc/multiqc_data/multiqc_software_versions.yaml", + "multiqc/multiqc_data/multiqc_sources.yaml", + "multiqc/multiqc_data/porechop.yaml", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/mqc_busco_plot_bacteria_odb10_1.pdf", + "multiqc/multiqc_plots/pdf/mqc_busco_plot_bacteria_odb10_1_pc.pdf", + "multiqc/multiqc_plots/pdf/mqc_nanostat_quality_dist_1.pdf", + "multiqc/multiqc_plots/pdf/mqc_nanostat_quality_dist_1_pc.pdf", + "multiqc/multiqc_plots/pdf/mqc_porechop-endtrim-barplot_1.pdf", + "multiqc/multiqc_plots/pdf/mqc_porechop-endtrim-barplot_1_pc.pdf", + "multiqc/multiqc_plots/pdf/mqc_porechop-middlesplit-barplot_1.pdf", + 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with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/long_dragonflye.nf.test.snap b/tests/long_dragonflye.nf.test.snap new file mode 100644 index 00000000..69b80c1c --- /dev/null +++ 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workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/long_liftoff.nf.test.snap b/tests/long_liftoff.nf.test.snap new file mode 100644 index 00000000..12962f22 --- /dev/null +++ b/tests/long_liftoff.nf.test.snap @@ -0,0 +1,411 @@ +{ + "-profile test_liftoff": { + "content": [ + 14, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "FASTP": { + "fastp": "0.23.4" + }, + "FASTQC_RAW": { + "fastqc": "0.12.1" + }, + "FASTQC_TRIM": { + "fastqc": "0.12.1" + }, + "LIFTOFF": { + "liftoff": "v1.6.3" + }, + "QUAST": { + "quast": "5.2.0" + }, + "UNICYCLER": 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"mqc_fastp-seq-quality-plot_Read_1_After_filtering.yaml:md5,b6d62af1e24d74cfc8860e2c3bb1e1f8", + "mqc_fastp-seq-quality-plot_Read_1_Before_filtering.yaml:md5,8a2f99badd4307372fbf3cbad6d0ea1d", + "mqc_fastp-seq-quality-plot_Read_2_After_filtering.yaml:md5,b6cd211a33c6a5ea2f33ba0b8bff2e12", + "mqc_fastp-seq-quality-plot_Read_2_Before_filtering.yaml:md5,53b11895fa7b0f3a217c6d08b656edde", + "mqc_fastp_filtered_reads_plot_1.yaml:md5,8b8ca8b9b2ba74ff4878848ccc7a0c1f", + "mqc_fastqc_adapter_content_plot_1.yaml:md5,03765b759de8ca659af65aa226a0c91b", + "mqc_fastqc_per_base_n_content_plot-2_1.yaml:md5,133136f55a621314f29395b0b590e02c", + "mqc_fastqc_per_base_n_content_plot_1.yaml:md5,7c8cebddb77c63cf63e31c559c02c9fa", + "mqc_fastqc_per_base_sequence_quality_plot-2_1.yaml:md5,c36608746f280013ed31fe1d3b6059de", + "mqc_fastqc_per_base_sequence_quality_plot_1.yaml:md5,8b543fd862b00615123e5a62be0d5099", + "mqc_fastqc_per_sequence_gc_content_plot-2_Counts.yaml:md5,a9e7955b572fcb86414dd273c648141f", + "mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.yaml:md5,ec175b43fc74064aac53695244cd47d7", + "mqc_fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,786db52131724d97f598f14b17e15e1c", + "mqc_fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,569ff6b6eee59b26ce354b4b93f2fdc4", + "mqc_fastqc_per_sequence_quality_scores_plot-2_1.yaml:md5,6a83696e544a9d39db9231efc91915ad", + "mqc_fastqc_per_sequence_quality_scores_plot_1.yaml:md5,e9012a938a3e11c0bd9847d18273fe88", + "mqc_fastqc_sequence_counts_plot-2_1.yaml:md5,9c4bf16973d87cfe3731b660fffb4ddb", + "mqc_fastqc_sequence_counts_plot_1.yaml:md5,a940e04693bcbadf20405148a1b1be35", + "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,904ae9ce7abc638239879b6d16ff80a8", + "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,4839cd6c3bd11763f6f58ec0c1fd75b2", + "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,2a0bfc0ec257081a52bf4f1755dd246b", + "mqc_quast_num_contigs_1.yaml:md5,98c3bbef635dac3f5afe78c1f6718e5e", + "multiqc_busco.yaml:md5,003b890081970ec29305149c67f67cc9", + "multiqc_citations.yaml:md5,e46f6ed003947fe967edd4674a82d4c6", + "multiqc_fastp.yaml:md5,562cb7689bb8074a7bca26ae8a129996", + "multiqc_fastqc.yaml:md5,05172556a25feb1277e789e91031d3bc", + "multiqc_fastqc_1.yaml:md5,a4bc353bd4a67c1f480fb890d806bf6a", + "multiqc_general_stats.yaml:md5,c1a9086493cf9a79e03a29941dbddd85", + "multiqc_quast.yaml:md5,ae6477bf080e3c3cd57bef7a5e2e6255", + "ERR044595.fastp.json:md5,ab69a1d8f62b6e1be76c83bb1022e882", + "ERR064912.fastp.json:md5,b79afd61a88a0637d49b78537c2938e8" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.2" + }, + "timestamp": "2025-07-07T19:15:59.829768165" + } +} \ No newline at end of file diff --git a/tests/long_miniasm.nf.test b/tests/long_miniasm.nf.test new file mode 100644 index 00000000..af4410a6 --- /dev/null +++ b/tests/long_miniasm.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_long_miniasm" + + test("-profile test_long_miniasm") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/long_miniasm.nf.test.snap b/tests/long_miniasm.nf.test.snap new file mode 100644 index 00000000..88ed5366 --- /dev/null +++ b/tests/long_miniasm.nf.test.snap @@ -0,0 +1,382 @@ +{ + "-profile test_long_miniasm": { + "content": [ + 14, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "KRAKEN2_DB_PREPARATION": { + "tar": null + }, + "KRAKEN2_LONG": { + "kraken2": "2.1.2", + "pigz": 2.6 + }, + "MEDAKA": { + "medaka": "1.4.3" + }, + "MINIASM": { + "miniasm": "0.3-r179" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.24-r1122" + }, + "MINIMAP2_CONSENSUS": { + "minimap2": "2.24-r1122" + }, + "NANOPLOT": { + "nanoplot": "1.41.6" + }, + "PORECHOP_PORECHOP": { + "porechop": "0.2.4" + }, + "PROKKA": { + "prokka": "1.14.6" + }, + "QUAST": { + "quast": "5.2.0" + }, + "RACON": { + "racon": "1.4.20" + }, + "TOULLIGQC": { + "toulligqc": "2.5.6" + }, + "Workflow": { + "nf-core/bacass": "v2.5.0dev" + } + }, + [ + "Medaka", + "Medaka/TestMe_polished_genome.fa", + "Miniasm", + "Miniasm/TestMe.consensus.fasta.gz", + "Miniasm/TestMe.fasta.gz", + "Prokka", + "Prokka/TestMe", + "Prokka/TestMe/TestMe.err", + "Prokka/TestMe/TestMe.faa", + "Prokka/TestMe/TestMe.ffn", + "Prokka/TestMe/TestMe.fna", + "Prokka/TestMe/TestMe.fsa", + "Prokka/TestMe/TestMe.gbk", + "Prokka/TestMe/TestMe.gff", + "Prokka/TestMe/TestMe.log", + "Prokka/TestMe/TestMe.sqn", + "Prokka/TestMe/TestMe.tbl", + "Prokka/TestMe/TestMe.tsv", + "Prokka/TestMe/TestMe.txt", + "QC_longreads", + "QC_longreads/NanoPlot", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_dot.png", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", + "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", + "QC_longreads/NanoPlot/NanoPlot-report.html", + "QC_longreads/NanoPlot/NanoPlot_20250707_1916.log", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/TestMe.txt", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedHistogramReadlength.png", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.html", + "QC_longreads/NanoPlot/WeightedLogTransformed_HistogramReadlength.png", + "QC_longreads/NanoPlot/Yield_By_Length.html", + "QC_longreads/NanoPlot/Yield_By_Length.png", + "QC_longreads/ToulligQC", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Channel_occupancy_of_the_flowcell.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Correlation_between_read_length_and_PHRED_score.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Distribution_of_read_lengths.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/PHRED_score_density_distribution.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/PHRED_score_distribution.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/PHRED_score_over_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Read_count_histogram.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Read_length_over_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Yield_plot_through_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/plotly.min.js", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/report.data", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/report.html", + "QUAST", + "QUAST/report", + "QUAST/report/basic_stats", + "QUAST/report/basic_stats/GC_content_plot.pdf", + "QUAST/report/basic_stats/Nx_plot.pdf", + "QUAST/report/basic_stats/TestMe_polished_genome_GC_content_plot.pdf", + "QUAST/report/basic_stats/cumulative_plot.pdf", + "QUAST/report/icarus.html", + "QUAST/report/icarus_viewers", + "QUAST/report/icarus_viewers/contig_size_viewer.html", + "QUAST/report/quast.log", + "QUAST/report/report.html", + "QUAST/report/report.pdf", + "QUAST/report/report.tex", + "QUAST/report/report.tsv", + "QUAST/report/report.txt", + "QUAST/report/transposed_report.tex", + "QUAST/report/transposed_report.tsv", + "QUAST/report/transposed_report.txt", + "busco", + "busco/TestMe-bacteria_odb10-busco", + "busco/TestMe-bacteria_odb10-busco.batch_summary.txt", + "busco/TestMe-bacteria_odb10-busco.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/bbtools_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/bbtools_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/hmmsearch_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/hmmsearch_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/prodigal_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/logs/prodigal_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/.checkpoint", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/predicted.faa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/predicted.fna", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/.bbtools_output", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/full_table.tsv", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/missing_busco_list.tsv", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/short_summary.json", + "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/short_summary.txt", + "busco/TestMe-bacteria_odb10-busco/logs", + "busco/busco_downloads", + "busco/short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json", + "busco/short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt", + "kraken2", + "kraken2/TestMe_longreads.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/mqc_busco_plot_bacteria_odb10_1.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Class.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Domain.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Family.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Genus.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Order.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Phylum.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Root.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Species.yaml", + "multiqc/multiqc_data/mqc_kraken-top-n-plot_Unclassified.yaml", + "multiqc/multiqc_data/mqc_nanostat_quality_dist_1.yaml", + "multiqc/multiqc_data/mqc_porechop-endtrim-barplot_1.yaml", + "multiqc/multiqc_data/mqc_porechop-middlesplit-barplot_1.yaml", + "multiqc/multiqc_data/mqc_porechop-starttrim-barplot_1.yaml", + "multiqc/multiqc_data/mqc_prokka_plot_1.yaml", + "multiqc/multiqc_data/mqc_quast_num_contigs_1.yaml", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_busco.yaml", + "multiqc/multiqc_data/multiqc_citations.yaml", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.yaml", + "multiqc/multiqc_data/multiqc_kraken.yaml", + "multiqc/multiqc_data/multiqc_nanostat.yaml", + "multiqc/multiqc_data/multiqc_prokka.yaml", + "multiqc/multiqc_data/multiqc_quast.yaml", + "multiqc/multiqc_data/multiqc_software_versions.yaml", + "multiqc/multiqc_data/multiqc_sources.yaml", + "multiqc/multiqc_data/porechop.yaml", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/mqc_busco_plot_bacteria_odb10_1.pdf", + "multiqc/multiqc_plots/pdf/mqc_busco_plot_bacteria_odb10_1_pc.pdf", + "multiqc/multiqc_plots/pdf/mqc_kraken-top-n-plot_Class.pdf", + "multiqc/multiqc_plots/pdf/mqc_kraken-top-n-plot_Class_pc.pdf", + "multiqc/multiqc_plots/pdf/mqc_kraken-top-n-plot_Domain.pdf", + 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b/tests/long_miniasm_prokka.nf.test new file mode 100644 index 00000000..897b9cb9 --- /dev/null +++ b/tests/long_miniasm_prokka.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + profile "test_long_miniasm_prokka" + + test("-profile test_long_miniasm_prokka") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_bacass_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/long_miniasm_prokka.nf.test.snap b/tests/long_miniasm_prokka.nf.test.snap new file mode 100644 index 00000000..df955d72 --- /dev/null +++ b/tests/long_miniasm_prokka.nf.test.snap @@ -0,0 +1,572 @@ +{ + "-profile test_long_miniasm_prokka": { + "content": [ + 12, + { + "BUSCO_BUSCO": { + "busco": "5.8.3" + }, + "MEDAKA": { + "medaka": "1.4.3" + }, + "MINIASM": { + "miniasm": "0.3-r179" + }, + "MINIMAP2_ALIGN": { + "minimap2": "2.24-r1122" + }, + "MINIMAP2_CONSENSUS": { + "minimap2": "2.24-r1122" + }, + "NANOPLOT": { + "nanoplot": "1.41.6" + }, + "PORECHOP_PORECHOP": { + "porechop": "0.2.4" + }, + "PROKKA": { + "prokka": "1.14.6" + }, + "QUAST": { + "quast": "5.2.0" + }, + "RACON": { + "racon": "1.4.20" + }, + 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"Non_weightedLogTransformed_HistogramReadlength.png:md5,7a81280b5d06ec9fd8a3322edee55426", + "TestMe.txt:md5,9026fca74ef9bf4de88094c47ffe0c86", + "WeightedHistogramReadlength.html:md5,9cfac0d8c7cfd2ae3617afbfc24b0316", + "WeightedHistogramReadlength.png:md5,d7a3929470c4d538e2688b5b553e133f", + "WeightedLogTransformed_HistogramReadlength.html:md5,e5ff7d1244fe94152b25ab81d47ff12f", + "WeightedLogTransformed_HistogramReadlength.png:md5,96d5e46ee816c396f53b14ec414e3924", + "Yield_By_Length.html:md5,fe2e84d11e0bdd0aaa7d0bba1e96659b", + "Yield_By_Length.png:md5,0601420f5e008f9b297c0e74489cb8aa", + "Channel_occupancy_of_the_flowcell.html:md5,9df0630f5788e09db43a52cec9b267b7", + "Correlation_between_read_length_and_PHRED_score.html:md5,70657ad403bb1cf7dbaafc53572299a0", + "Distribution_of_read_lengths.html:md5,daccc8e68b8df2deaed9d2a8e05ec26f", + "PHRED_score_density_distribution.html:md5,991f94509d7a6438566ffab72f259666", + "PHRED_score_distribution.html:md5,3eb5adf82db7ec35a5f0a3b1dcbd3126", + "PHRED_score_over_time.html:md5,abd83ab40bebfb34f1e677c5d3096902", + "Read_count_histogram.html:md5,c10074d723ef1e51cf0b94aadb805183", + "Read_length_over_time.html:md5,f7cbdbf5d30295f6e0f662c534b01ed0", + "Yield_plot_through_time.html:md5,22d12b164293bb6b622f3d88365c7e5d", + "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", + "report.data:md5,78d9d8e1a5073a6d3bc5e2825c2f55f6", + "report.html:md5,65d8e0a5e0e3e363424f0de9f30ee343", + "TestMe-bacteria_odb10-busco.log:md5,0304404e16ca1c5b524ce922039ff90c", + "predicted.faa:md5,d9d8ade611d7a2fc3dc3a26e50638ffa", + "predicted.fna:md5,0f499c98f12995a07285325de70e14c3", + "prodigal_mode_meta_code_11.faa:md5,e3c377dde8a3bb549aa8ee10a5012f5d", + "prodigal_mode_meta_code_11.fna:md5,0f499c98f12995a07285325de70e14c3", + "prodigal_mode_meta_code_4.faa:md5,e3c377dde8a3bb549aa8ee10a5012f5d", + "prodigal_mode_meta_code_4.fna:md5,0f499c98f12995a07285325de70e14c3", + "full_table.tsv:md5,0e7e88ec9a00f2911e5e2826a2c55d21", + "missing_busco_list.tsv:md5,ee72fcf3b896bca75487a26d348631a2", + "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json:md5,afd2a41ceef08d6dd1830c21261e6137", + "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt:md5,2fde2d9e0ade56aebe033e47a179e7cd", + "mqc_busco_plot_bacteria_odb10_1.yaml:md5,b0c60571185671c3a7a17280e257dee9", + "mqc_nanostat_quality_dist_1.yaml:md5,4c825adfe187004dec6e2438f001c422", + "mqc_porechop-endtrim-barplot_1.yaml:md5,711a2deae67088db22b1a2a462da4969", + "mqc_porechop-middlesplit-barplot_1.yaml:md5,dab7cce19986f3193484fd241075b221", + "mqc_porechop-starttrim-barplot_1.yaml:md5,d179142c064a1ab5d0d5eca777400982", + "mqc_prokka_plot_1.yaml:md5,fb6137b5f171620b3252ecc4a4687815", + "mqc_quast_num_contigs_1.yaml:md5,27fda5a380cac71274b9b6232f3d0a9a", + "multiqc_busco.yaml:md5,c3eb539eb1f80483d02d72f7a7ec3844", + "multiqc_citations.yaml:md5,80450f20190a42871cb64f62ae9bec3e", + "multiqc_general_stats.yaml:md5,4f99c61498841ec9ab898756d3c1e750", + "multiqc_nanostat.yaml:md5,199cc0d2dc4e425e371774b94ab38741", + "multiqc_prokka.yaml:md5,a2835805534e502fa4534c9e40a8aa5e", + "multiqc_quast.yaml:md5,4ac7024bfc6a590897231c9049bffed1", + "porechop.yaml:md5,02877aea8bb09d59145fc79a3c4f3115", + "TestMe.porechop.log:md5,ea7abbf36e95282491fc6f205aac64c7" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.2" + }, + "timestamp": "2025-07-07T19:22:07.100607554" + } +} \ No newline at end of file From 15b5b7c72d856d238dc74473d769b0d4b4e3b8b1 Mon Sep 17 00:00:00 2001 From: d4straub Date: Tue, 8 Jul 2025 11:08:46 +0200 Subject: [PATCH 2/5] reduce md5sum checks --- tests/.nftignore | 21 ++++--- tests/.nftignore_files_entirely | 2 + tests/default.nf.test.snap | 25 +------- tests/dfast.nf.test.snap | 29 +-------- tests/hybrid.nf.test | 2 +- tests/hybrid.nf.test.snap | 71 +--------------------- tests/hybrid_dragonflye.nf.test | 2 +- tests/hybrid_dragonflye.nf.test.snap | 65 +------------------- tests/long.nf.test | 2 +- tests/long.nf.test.snap | 77 +----------------------- tests/long_dragonflye.nf.test | 2 +- tests/long_dragonflye.nf.test.snap | 79 +------------------------ tests/long_liftoff.nf.test.snap | 23 +------- tests/long_miniasm.nf.test | 2 +- tests/long_miniasm.nf.test.snap | 73 +---------------------- tests/long_miniasm_prokka.nf.test.snap | 82 ++++++-------------------- 16 files changed, 49 insertions(+), 508 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 70ba825d..059516d1 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -6,19 +6,26 @@ multiqc/multiqc_data/multiqc_sources.{txt,yaml} multiqc/multiqc_data/multiqc_software_versions.{txt,yaml} multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html +multiqc/multiqc_data/mqc_prokka_plot_1.yaml +multiqc/multiqc_data/multiqc_prokka.yaml +multiqc/multiqc_data/multiqc_general_stats.yaml +multiqc/multiqc_data/mqc_quast_num_contigs_1.yaml +multiqc/multiqc_data/multiqc_quast.yaml +multiqc/multiqc_data/porechop.yaml fastqc/*_fastqc.{html,zip} FastQC/raw/*.{html,zip} FastQC/trim/*.{html,zip} pipeline_info/*.{html,json,txt,yml} -busco/busco_downloads/** -busco/**/busco_sequences/** -busco/**/hmmer_output/** -busco/*.batch_summary.txt -busco/**/*.{log,checkpoint} -busco/**/short_summary.*{txt,json} -busco/*.batch_summary.txt +busco/** +busco/* trimming/shortreads/json_html/*.fastp.html trimming/shortreads/log/*.fastp.log +trimming/longreads/porechop/*.porechop.log Prokka/*/*.{gbk,sqn,log,err} QUAST/report/** Unicycler/*.unicycler.log +DFAST/*/*.{tsv,log,gbk} +QC_longreads/ToulligQC/** +QC_longreads/NanoPlot/* +Dragonflye/* +Medaka/* diff --git a/tests/.nftignore_files_entirely b/tests/.nftignore_files_entirely index f60be8da..4dcbb06a 100644 --- a/tests/.nftignore_files_entirely +++ b/tests/.nftignore_files_entirely @@ -3,3 +3,5 @@ pipeline_info/*.{html,json,txt} busco/busco_downloads/** busco/**/busco_sequences/** busco/**/hmmer_output/** +QC_longreads/ToulligQC/** +QC_longreads/NanoPlot/*.log diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 7f96c3ea..2b06bd32 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -375,24 +375,6 @@ "ERR044595.scaffolds.fa.gz:md5,347f2de2f160832fb7a63fe9e7730e66", "ERR064912.assembly.gfa.gz:md5,d3ad512273883e85aab9ae52e07eb0b8", "ERR064912.scaffolds.fa.gz:md5,067f5be263d706a08b8d578e89d724d8", - "ERR044595-bacteria_odb10-busco.log:md5,d8d1fa42436fab79b8a8c6a30882c16b", - "predicted.faa:md5,db8e8b87c70d237aa46e2cc846877482", - "predicted.fna:md5,47176bfbae23f4c143ef3cacb1a04649", - "prodigal_mode_single_code_11.faa:md5,0c39e1386af4eff58bea4b39e67ba5a0", - "prodigal_mode_single_code_11.fna:md5,47176bfbae23f4c143ef3cacb1a04649", - "full_table.tsv:md5,7d14920eee576b479a326c322fd8bcc3", - "missing_busco_list.tsv:md5,d90b0a5515b066e4d7a76f3dae9474b8", - "ERR064912-bacteria_odb10-busco.log:md5,562a878bd518be9d353e98ae5baddb7b", - "predicted.faa:md5,682b87bb8a8d677ed02ba2aa31fb07ff", - "predicted.fna:md5,7d21072bdfc82afeb7180e01a02b786f", - "prodigal_mode_single_code_11.faa:md5,bf97761e1b9bcac6f838a24d50de6c2f", - "prodigal_mode_single_code_11.fna:md5,7d21072bdfc82afeb7180e01a02b786f", - "full_table.tsv:md5,73afd7a0b817b1cd64ee71a6e4ea4bcd", - "missing_busco_list.tsv:md5,4cf87529bc0c6d1f3050e635653948dc", - "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.json:md5,34cdcc175fec96077a9939f3cb82c362", - "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.txt:md5,d2e0ca4b1d89cce2f99a538a7384ea3b", - "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.json:md5,7d29e4d61a7b04c81afcc8581fc81cef", - "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.txt:md5,b17547d30049b5e626d3463a32e46190", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,2e1c897d672181a4ee893911dc23b679", "mqc_fastp-insert-size-plot_1.yaml:md5,1da35415f0542ec3d3f6d6d7d250ae32", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,23ace34b503b638ef667647f7de2020a", @@ -424,16 +406,11 @@ "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,976809542688e7298f3aad6a179eab48", "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,0d7cae663635dc332ea80514ffc7d3d2", "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,f10ae65942541fa331f9e3f840da2478", - "mqc_prokka_plot_1.yaml:md5,c6449e694bc5c8d551f27fc46c1d6c95", - "mqc_quast_num_contigs_1.yaml:md5,329eb87240c6e7840e91aeec952d34ac", "multiqc_busco.yaml:md5,929d2dcdb46aaba007a75fd3a58ab6dd", "multiqc_citations.yaml:md5,0842be95dd6c2081198f682f370c7f0a", "multiqc_fastp.yaml:md5,76a57b9c81dd4125a92ad036ae9daf49", "multiqc_fastqc.yaml:md5,4c4e1b713139eef4b82e3aa9e6dbaca2", "multiqc_fastqc_1.yaml:md5,1136cc6159989b6675b324746d67c3f1", - "multiqc_general_stats.yaml:md5,d2d9a5c4102b11bb0e05dc0732fb4552", - "multiqc_prokka.yaml:md5,dab5276a3c011eeb6ddb205d8f7e9c71", - "multiqc_quast.yaml:md5,0059c2c892277cbde01e7bd5a17b4a06", "ERR044595.fastp.json:md5,75fdd7a9ef72dfd289e5dc18618949b7", "ERR064912.fastp.json:md5,b79afd61a88a0637d49b78537c2938e8" ] @@ -442,6 +419,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T17:47:19.529150043" + "timestamp": "2025-07-08T09:21:11.466376456" } } \ No newline at end of file diff --git a/tests/dfast.nf.test.snap b/tests/dfast.nf.test.snap index d85fc8b9..d4eb2386 100644 --- a/tests/dfast.nf.test.snap +++ b/tests/dfast.nf.test.snap @@ -343,52 +343,28 @@ "trimming/shortreads/log/ERR064912.fastp.log" ], [ - "application.log:md5,ad082d1de01b97b88921101c45661bae", "cds.fna:md5,094f344fd6e124a930a16defb52fb981", "mss.ann:md5,0959c20742079a18f19b28fdaef35e5b", "mss.fasta:md5,84d583d37198c32f8752c2023d15ae24", "genome.embl:md5,ea00a5a8aa5ade0c0f872bb0dca96976", "genome.fna:md5,f7ee0733af225115b84b0c9fa2592d31", - "genome.gbk:md5,dec5cd95ac895f4257de004005eb3795", "genome.gff:md5,acbd86770d4745b8141717b96d265cb4", "protein.faa:md5,e4cb3336221d3ec01e359c466a0b10f3", - "pseudogene_summary.tsv:md5,3814520cdacb97507dedd4cbd78ae8ea", "rna.fna:md5,d41d8cd98f00b204e9800998ecf8427e", "statistics.txt:md5,5fadaa716422618671bb4e3fa28a74cb", - "application.log:md5,5e39dfa018b3cae4cf170405fa6037a6", "cds.fna:md5,b822b2067bae852991513661c6881b8c", "mss.ann:md5,b03b5411b9cd4eca807380fd7f2e1413", "mss.fasta:md5,fc5fb0a452a7b3495b7e9c52d2aa0f74", "genome.embl:md5,b8533b6df15b44a92e275d9a4d2aa7cc", "genome.fna:md5,b10166345264464d85d78f47247150af", - "genome.gbk:md5,3ca5e8c1014bc1c82757a2eaf3a3bbbd", "genome.gff:md5,79bf494d80e7e933cd6f7a863b999e7e", "protein.faa:md5,1f7fc9df6262bee25dc00983837979b4", - "pseudogene_summary.tsv:md5,393f90b283b233e12c3b06bd9483ff64", "rna.fna:md5,d41d8cd98f00b204e9800998ecf8427e", "statistics.txt:md5,0526ab9f02c4a3d51b51b9736a9f7bad", "ERR044595.assembly.gfa.gz:md5,bc898821edeaf84029c214d9870df9c1", "ERR044595.scaffolds.fa.gz:md5,5607023f2e453ce5da9f0a36780bba60", "ERR064912.assembly.gfa.gz:md5,d3ad512273883e85aab9ae52e07eb0b8", "ERR064912.scaffolds.fa.gz:md5,067f5be263d706a08b8d578e89d724d8", - "ERR044595-bacteria_odb10-busco.log:md5,081608c303932cf23d05c915f8d55a12", - "predicted.faa:md5,9167f01c56cbb72cbe7fa4da6b3b3710", - "predicted.fna:md5,7ae7cced219e8575e3cca063961ad999", - "prodigal_mode_single_code_11.faa:md5,5e5298de767b28054112fafb2a0a3604", - "prodigal_mode_single_code_11.fna:md5,7ae7cced219e8575e3cca063961ad999", - "full_table.tsv:md5,0520030619f1fe037a612d87a9d508d9", - "missing_busco_list.tsv:md5,4cf87529bc0c6d1f3050e635653948dc", - "ERR064912-bacteria_odb10-busco.log:md5,122927e574307ef800b91e00244e6a5a", - "predicted.faa:md5,682b87bb8a8d677ed02ba2aa31fb07ff", - "predicted.fna:md5,7d21072bdfc82afeb7180e01a02b786f", - "prodigal_mode_single_code_11.faa:md5,bf97761e1b9bcac6f838a24d50de6c2f", - "prodigal_mode_single_code_11.fna:md5,7d21072bdfc82afeb7180e01a02b786f", - "full_table.tsv:md5,73afd7a0b817b1cd64ee71a6e4ea4bcd", - "missing_busco_list.tsv:md5,4cf87529bc0c6d1f3050e635653948dc", - "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.json:md5,bc80b9804aa3bacd12b55cf32b42e24a", - "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.txt:md5,9125f1a772ab8a030305575e014cc5ec", - "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.json:md5,dca970897e0a7a0ff615838676747fa5", - "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.txt:md5,d102c0e1b17b6aa52d42aaf0f10402a9", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,d095cfa297352d240023df5030592c44", "mqc_fastp-insert-size-plot_1.yaml:md5,502eb7cce116025829ba91041bd8e06f", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,1626ad6d4b0e5c11b812eb28f010bb30", @@ -420,14 +396,11 @@ "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,904ae9ce7abc638239879b6d16ff80a8", "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,4839cd6c3bd11763f6f58ec0c1fd75b2", "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,2a0bfc0ec257081a52bf4f1755dd246b", - "mqc_quast_num_contigs_1.yaml:md5,98c3bbef635dac3f5afe78c1f6718e5e", "multiqc_busco.yaml:md5,003b890081970ec29305149c67f67cc9", "multiqc_citations.yaml:md5,e46f6ed003947fe967edd4674a82d4c6", "multiqc_fastp.yaml:md5,562cb7689bb8074a7bca26ae8a129996", "multiqc_fastqc.yaml:md5,05172556a25feb1277e789e91031d3bc", "multiqc_fastqc_1.yaml:md5,a4bc353bd4a67c1f480fb890d806bf6a", - "multiqc_general_stats.yaml:md5,c1a9086493cf9a79e03a29941dbddd85", - "multiqc_quast.yaml:md5,b6d3146c4a0fdf49d430d6df87cf2577", "ERR044595.fastp.json:md5,ab69a1d8f62b6e1be76c83bb1022e882", "ERR064912.fastp.json:md5,b79afd61a88a0637d49b78537c2938e8" ] @@ -436,6 +409,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T18:12:16.674942373" + "timestamp": "2025-07-08T09:47:10.680934718" } } \ No newline at end of file diff --git a/tests/hybrid.nf.test b/tests/hybrid.nf.test index bf98981a..2e87b71b 100644 --- a/tests/hybrid.nf.test +++ b/tests/hybrid.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/hybrid.nf.test.snap b/tests/hybrid.nf.test.snap index 013293bb..6c6078a0 100644 --- a/tests/hybrid.nf.test.snap +++ b/tests/hybrid.nf.test.snap @@ -74,7 +74,6 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250707_1812.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -86,20 +85,6 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Channel_occupancy_of_the_flowcell.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/PHRED_score_over_time.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Read_length_over_time.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/Yield_plot_through_time.html", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/images/plotly.min.js", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/report.data", - "QC_longreads/ToulligQC/ERR044595Toulligqc-report-2025-07-07-181235/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -371,55 +356,8 @@ "trimming/shortreads/log/ERR044595.fastp.log" ], [ - "ERR044595_polished_genome.fa:md5,f3195e3d7aed74b6f75a77e3f34c71ef", - "ERR044595.faa:md5,98de8fc97d1146100173418c8f22bce0", - "ERR044595.ffn:md5,562d09be60c0343d74742f45c51bd8cb", - "ERR044595.fna:md5,71769918493ca0fc25c00c50db260e14", - "ERR044595.fsa:md5,f3face5b4ccd17f943559342a4af9e07", - "ERR044595.gff:md5,6967ec505f9b98d92d6aec6a83ab0a2b", - "ERR044595.tbl:md5,8836a2ef15a7216b907a18c865cf72eb", - "ERR044595.tsv:md5,b774d0ac8624ae4c669cab9fe41a627c", - "ERR044595.txt:md5,6566b6ffe5beb2e078caf106c96f27ac", - "ERR044595.txt:md5,685beea7face13b1d520ce3203ee13d0", - "LengthvsQualityScatterPlot_dot.html:md5,33363de0c33d76708a6750846b11c85d", - "LengthvsQualityScatterPlot_dot.png:md5,f6fc97503e5e48d1b87acb30c8672bcc", - "LengthvsQualityScatterPlot_kde.html:md5,fcdeb69df7e71b3f022e641eafcc2e11", - "LengthvsQualityScatterPlot_kde.png:md5,37f9b96902f2cfc3bb8f36b33e87f792", - "NanoPlot-report.html:md5,aad8f4657a371a39dfdbfac92827ff6b", - "NanoPlot_20250707_1812.log:md5,2ee174f1485fbc61a7b43ab81d9e6ade", - "Non_weightedHistogramReadlength.html:md5,d3e446d12adcece8cf7a34b6c393401c", - "Non_weightedHistogramReadlength.png:md5,d2aeebc6ce8824a354502b46524087fd", - "Non_weightedLogTransformed_HistogramReadlength.html:md5,f2887774d1ef8684981a225d08d77f60", - "Non_weightedLogTransformed_HistogramReadlength.png:md5,3b867e8d0a478eb28ca8e0c8fd83f072", - "WeightedHistogramReadlength.html:md5,4bb68732501d8e56ae949c11c632b303", - "WeightedHistogramReadlength.png:md5,d48810de04b5e138841654570bfa4f0b", - "WeightedLogTransformed_HistogramReadlength.html:md5,1891a51ba2c7e2854cc45092890423e9", - "WeightedLogTransformed_HistogramReadlength.png:md5,21bb5cafd5f27b7baf56d8dd48b7f4ea", - "Yield_By_Length.html:md5,d47efdbcd1a497b55d320031937696f5", - "Yield_By_Length.png:md5,12037a7ba1fd29fa302b3369c2230f18", - "Channel_occupancy_of_the_flowcell.html:md5,7565623872e26da449f9fa80ff48826d", - "Correlation_between_read_length_and_PHRED_score.html:md5,5beb2853940decb0abd4e6905b3fedc9", - "Distribution_of_read_lengths.html:md5,fc895198573cb4c3e481b6338e88044a", - "PHRED_score_density_distribution.html:md5,d495f444f7a11f199e99d2bd7fd8de73", - "PHRED_score_distribution.html:md5,d95141068d1444bc31d17db50fe0e0f7", - "PHRED_score_over_time.html:md5,a9b82bb5607e466f2146c488f3534248", - "Read_count_histogram.html:md5,012bc34b1fc6037ac4ce74654afb27bd", - "Read_length_over_time.html:md5,ec02f672ee24c08436acb20064d51d06", - "Yield_plot_through_time.html:md5,69f360f364def6a7f8ff3983c674cee0", - "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", - "report.data:md5,59c2e49f13174b01f4d0268768d7e244", - "report.html:md5,1adf79d7d8bbbb394d96380cb36fd232", "ERR044595.assembly.gfa.gz:md5,bc898821edeaf84029c214d9870df9c1", "ERR044595.scaffolds.fa.gz:md5,5607023f2e453ce5da9f0a36780bba60", - "ERR044595-bacteria_odb10-busco.log:md5,b177ebbde07536310df5a2b7af279a81", - "predicted.faa:md5,9a76260e5eea39bc93439fe80a9aff27", - "predicted.fna:md5,373c8cdca8889b5edb45737bf0247514", - "prodigal_mode_single_code_11.faa:md5,12c2068b3718a1810d0b7a175fea2bfc", - "prodigal_mode_single_code_11.fna:md5,373c8cdca8889b5edb45737bf0247514", - "full_table.tsv:md5,0520030619f1fe037a612d87a9d508d9", - "missing_busco_list.tsv:md5,4cf87529bc0c6d1f3050e635653948dc", - "short_summary.specific.bacteria_odb10.ERR044595_polished_genome.fa.json:md5,aab2029aa44bbfe2a2dbd20503e9cec1", - "short_summary.specific.bacteria_odb10.ERR044595_polished_genome.fa.txt:md5,09409aa574714ac619889ad6b77db9d8", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,4226198a9300d1c31243aa23b32bf0fe", "mqc_fastp-insert-size-plot_1.yaml:md5,b361f3cadd080fbb7d4eaf3255ca8587", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,77982458bba1ca892c41c2917f11517e", @@ -455,19 +393,12 @@ "mqc_porechop-endtrim-barplot_1.yaml:md5,29573e9fc6174bb91352b0b9f248335f", "mqc_porechop-middlesplit-barplot_1.yaml:md5,844b018c7434ca59c893901eef530de8", "mqc_porechop-starttrim-barplot_1.yaml:md5,e6cced8fc844dabd795ba0dfa6ec0e64", - "mqc_prokka_plot_1.yaml:md5,4033ae78aa4b6e61b2b2925ab4122b80", - "mqc_quast_num_contigs_1.yaml:md5,fb56467c2cc7e7dfd50d6d306c7defd9", "multiqc_busco.yaml:md5,cc14257553d13289016474578391216c", "multiqc_citations.yaml:md5,c1962a840fe1cf1698fbdeb8953601ed", "multiqc_fastp.yaml:md5,c77f208bad399ef0250ae293a9d35a4e", "multiqc_fastqc.yaml:md5,68dcba3602303c17700845789c5228fb", "multiqc_fastqc_1.yaml:md5,9e5474735bdcccbaf6f2bd6039b1a4ee", - "multiqc_general_stats.yaml:md5,03cbcdcfa7fb04eab2640c7f54831b7e", "multiqc_nanostat.yaml:md5,b15cabc45adc271cd6d355ec18244ddc", - "multiqc_prokka.yaml:md5,8f1bc1653918ac57728dd2eb107615da", - "multiqc_quast.yaml:md5,b32bf4c828a4e8b5c6a6d1e51a700158", - "porechop.yaml:md5,7c5b60ab31a49def692703989e225413", - "ERR044595.porechop.log:md5,60d5a94c87e738472e0f9415fd89d8e8", "ERR044595.fastp.json:md5,ab69a1d8f62b6e1be76c83bb1022e882" ] ], @@ -475,6 +406,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T18:24:31.096595535" + "timestamp": "2025-07-08T09:59:21.268867867" } } \ No newline at end of file diff --git a/tests/hybrid_dragonflye.nf.test b/tests/hybrid_dragonflye.nf.test index fe2455b4..15874546 100644 --- a/tests/hybrid_dragonflye.nf.test +++ b/tests/hybrid_dragonflye.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**','**/mqc_quast_num_contigs_1.yaml','**/multiqc_quast.yaml']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/hybrid_dragonflye.nf.test.snap b/tests/hybrid_dragonflye.nf.test.snap index 9fc5dd0b..a8352397 100644 --- a/tests/hybrid_dragonflye.nf.test.snap +++ b/tests/hybrid_dragonflye.nf.test.snap @@ -77,7 +77,6 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250707_1825.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -89,16 +88,6 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/images/plotly.min.js", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/report.data", - "QC_longreads/ToulligQC/A1403KPNToulligqc-report-2025-07-07-182506/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -366,51 +355,6 @@ "trimming/shortreads/log/A1403KPN.fastp.log" ], [ - "A1403KPN.dragonflye.log:md5,ecc81bcc73fed0a9834a045ba123308c", - "A1403KPN.fa:md5,0cdbaebdcdea84c22d0bb192bf9f6145", - "A1403KPN_polished_genome.fa:md5,1dab8b5efa87149e4d79e38f82d24764", - "A1403KPN.faa:md5,e0dffdfc72f7bbf736a161d79b493ada", - "A1403KPN.ffn:md5,5296d2b55245502a0d251ba856f1072a", - "A1403KPN.fna:md5,611a220329fe5dab924c9df8805cabc0", - "A1403KPN.fsa:md5,3726d7ba341a21f115101162b382922c", - "A1403KPN.gff:md5,8ec5b99115b2108bdaa6bd91a77aed5a", - "A1403KPN.tbl:md5,02136ec422cc0f22153d0e062de5b61e", - "A1403KPN.tsv:md5,992fd18e4b72ad99c5ac8f8116383197", - "A1403KPN.txt:md5,46d5e7eda8e42719020de276839dbd1a", - "A1403KPN.txt:md5,f5a3d6ac4830e56aa10446b8b88924bf", - "LengthvsQualityScatterPlot_dot.html:md5,4f71bf7149e276efb4008ed9fb3ad21e", - "LengthvsQualityScatterPlot_dot.png:md5,84b993c788c579c01e139f5ce0dc11f8", - "LengthvsQualityScatterPlot_kde.html:md5,dae27dfe8541b1cb84f8edab09de757c", - "LengthvsQualityScatterPlot_kde.png:md5,be9593adccee848e4d0d028497793461", - "NanoPlot-report.html:md5,d40b06f1aeba0d71314d750c3bc52bad", - "NanoPlot_20250707_1825.log:md5,7196b08094d8982edffc233bfe33204e", - "Non_weightedHistogramReadlength.html:md5,5339573207bcbbddb67d46202b928c57", - "Non_weightedHistogramReadlength.png:md5,843c66b27ffb70d03a8f473c83091058", - "Non_weightedLogTransformed_HistogramReadlength.html:md5,a3f98e9a38231cc6df28d2d1f2fd0c1a", - "Non_weightedLogTransformed_HistogramReadlength.png:md5,7be63ffb9878ba750c0f1cbd016e3d4d", - "WeightedHistogramReadlength.html:md5,d5545f2f3b02f958d57345b2d84dcae6", - "WeightedHistogramReadlength.png:md5,a8347588979464c04b62c5e4c9bb4188", - "WeightedLogTransformed_HistogramReadlength.html:md5,4226ba9c3b69d4be2bea81f12904c8d3", - "WeightedLogTransformed_HistogramReadlength.png:md5,debea5690502857dd44a36f3cb49932d", - "Yield_By_Length.html:md5,d8b8195e00cc6394715017b6021f60cc", - "Yield_By_Length.png:md5,704c5eb8b12583270129e08c7e5f9e89", - "Correlation_between_read_length_and_PHRED_score.html:md5,8b6f00365e6cc0debe106c753cf705b2", - "Distribution_of_read_lengths.html:md5,4b10efcd067a1a2b6e3fa0495527a3ae", - "PHRED_score_density_distribution.html:md5,efa88a78f6d0cdfe3fa1ed0b4943ee3a", - "PHRED_score_distribution.html:md5,2c2d224cf0d5ad08e01647c7e86d8395", - "Read_count_histogram.html:md5,5a11779f2725ccbfebf428da6eab31ec", - "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", - "report.data:md5,d786ee0e9972d8363e15205deebea984", - "report.html:md5,b16d7fee7d1493e1abb4af4bccfbe111", - "A1403KPN-bacteria_odb10-busco.log:md5,a37919d3bb8abf595edcd907076c0f08", - "predicted.faa:md5,e20cc72628aebe67da0bb1e5510486b2", - "predicted.fna:md5,7bc69d75145af61052e561d662b058c6", - "prodigal_mode_single_code_11.faa:md5,5acb516f2cec20bb993c344085d6dcc4", - "prodigal_mode_single_code_11.fna:md5,7bc69d75145af61052e561d662b058c6", - "full_table.tsv:md5,df3e9ac25b434ca7e2e501defd6e52c9", - "missing_busco_list.tsv:md5,a1233de385a24f9a14b1a40c6fdf4484", - "short_summary.specific.bacteria_odb10.A1403KPN_polished_genome.fa.json:md5,d5ccf8b7d9c8984a2b57ac8cf3d6803c", - "short_summary.specific.bacteria_odb10.A1403KPN_polished_genome.fa.txt:md5,70c905e665983b0473a7b26883e879cb", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,f518abd2780ef768903dd5da62548fdb", "mqc_fastp-insert-size-plot_1.yaml:md5,57eb8863c4b8db578660ab66c341ab07", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,b44852244e0643016e4b83c6bd507ac3", @@ -446,19 +390,12 @@ "mqc_porechop-endtrim-barplot_1.yaml:md5,a6396edf17f4e4ed9954cda933af2b7b", "mqc_porechop-middlesplit-barplot_1.yaml:md5,5e89ca1f45fb6876b58ddbb20b86ea77", "mqc_porechop-starttrim-barplot_1.yaml:md5,34e8d91183bd582532ac654e8e287945", - "mqc_prokka_plot_1.yaml:md5,263db317035745f5925103b1c09883cb", - "mqc_quast_num_contigs_1.yaml:md5,ddacf823d2fd44a8d39d62b3d8b36a06", "multiqc_busco.yaml:md5,b645040c8295ca4a3b63af126dc68633", "multiqc_citations.yaml:md5,c1962a840fe1cf1698fbdeb8953601ed", "multiqc_fastp.yaml:md5,ed975e259ac4db3e9c2ba4dcd618fc18", "multiqc_fastqc.yaml:md5,a0b5fd24bb745bb77511c1962086fcf0", "multiqc_fastqc_1.yaml:md5,daf5f34bdacbbc207f86fc95768ce9a2", - "multiqc_general_stats.yaml:md5,91adec7ffafa3963479c557acde9245f", "multiqc_nanostat.yaml:md5,c9346968eeb2741d12322c9a5bb0c6c2", - "multiqc_prokka.yaml:md5,96845fe8945572f8a7df13228f75ba9b", - "multiqc_quast.yaml:md5,145f1ceae2b16c1e86d73d8ee7e44b87", - "porechop.yaml:md5,eee3e2eb251a026d42d70720da49fb4d", - "A1403KPN.porechop.log:md5,552282af03b80736e49b39466e9ba4b5", "A1403KPN.fastp.json:md5,be3cb43a0cfe3d2bd4990953318262d2" ] ], @@ -466,6 +403,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T18:39:53.525898974" + "timestamp": "2025-07-08T10:12:45.188352097" } } \ No newline at end of file diff --git a/tests/long.nf.test b/tests/long.nf.test index 3f762164..57ccc4f5 100644 --- a/tests/long.nf.test +++ b/tests/long.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**','**/multiqc_busco.yaml','**/mqc_busco_plot_*.yaml']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/long.nf.test.snap b/tests/long.nf.test.snap index 0ea564e5..637e3f2b 100644 --- a/tests/long.nf.test.snap +++ b/tests/long.nf.test.snap @@ -55,7 +55,6 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250707_1840.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -68,20 +67,6 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Channel_occupancy_of_the_flowcell.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/PHRED_score_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Read_length_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/Yield_plot_through_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/images/plotly.min.js", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/report.data", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184018/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -219,78 +204,20 @@ "trimming/longreads/porechop/TestMe.porechop.log" ], [ - "TestMe_polished_genome.fa:md5,540227635ff30f0225ea4be62ed29df5", - "TestMe.faa:md5,e8267b3a57e7a8759acf7446f28e4f12", - "TestMe.ffn:md5,b9428be09777ab33ae96c34002d01a46", - "TestMe.fna:md5,780d2cd163b003645da0dd4998ca872f", - "TestMe.fsa:md5,80b7be16bb312acd27138b7d0b067371", - "TestMe.gff:md5,70323662b261a59d71d586237fc3b1dd", - "TestMe.tbl:md5,f0223eba7cda9883f2a365f1a3c0cd57", - "TestMe.tsv:md5,0605e0223288cc5b0ef26751eaa03d8b", - "TestMe.txt:md5,7d512699ecf2377b41dddf5528a6074f", - "LengthvsQualityScatterPlot_dot.html:md5,55b524399e0149f24214812d9326935f", - "LengthvsQualityScatterPlot_dot.png:md5,7ba5cb54c5f7689a1b05f2a6e0b412c4", - "LengthvsQualityScatterPlot_kde.html:md5,118317b44f1a379ec6d6d839ef9acd01", - "LengthvsQualityScatterPlot_kde.png:md5,ec2880cdcc6d05e993eb0f0ebd736d88", - "NanoPlot-report.html:md5,2384a483bfcd72341f36ac161eb882fc", - "NanoPlot_20250707_1840.log:md5,d3d4981e5240354243d13d677ba2a3e4", - "Non_weightedHistogramReadlength.html:md5,cd0ca0b4e82182718fcc455ad73e4185", - "Non_weightedHistogramReadlength.png:md5,4a88af0963bea753816871ab2415c146", - "Non_weightedLogTransformed_HistogramReadlength.html:md5,0684e1de9aa7df07bcb2564d32df851b", - "Non_weightedLogTransformed_HistogramReadlength.png:md5,45cf40406afcd811446dee42e7bce6de", - "TestMe.txt:md5,07cbf8b60376bfec28d3dfdbadc7d0e9", - "WeightedHistogramReadlength.html:md5,3051616b7131948213a60208972fd414", - "WeightedHistogramReadlength.png:md5,781f3c14ffd74744a7534e5b4d5135a1", - "WeightedLogTransformed_HistogramReadlength.html:md5,34c35e7263a7c8672e86745fb180785f", - "WeightedLogTransformed_HistogramReadlength.png:md5,206cc08d2f5e84dbd24300566c144c31", - "Yield_By_Length.html:md5,9d01569ea31b35b370da67d1034f965f", - "Yield_By_Length.png:md5,3d53873f120f37fde9a541b17a23d69b", - "Channel_occupancy_of_the_flowcell.html:md5,1da684e85348e832a803f9bfc77a7b5c", - "Correlation_between_read_length_and_PHRED_score.html:md5,3ef3c1594414ff514498804110de2d2a", - "Distribution_of_read_lengths.html:md5,a7a4e53cee2f575edc8282588e3a9fe6", - "PHRED_score_density_distribution.html:md5,c540c14194c1e8aed4673c6aea281dbc", - "PHRED_score_distribution.html:md5,d09c3bb0088db08f541e73c6517d6481", - "PHRED_score_over_time.html:md5,99e3dc72b36d513411f09579a9416e91", - "Read_count_histogram.html:md5,a4d42e02d53a5245da663eefa6ca7c0e", - "Read_length_over_time.html:md5,34f871d1404671bdf92529eb765c0804", - "Yield_plot_through_time.html:md5,7bb5724d3063d58c36ab2e4dde8eae25", - "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", - "report.data:md5,ae842a9158d8fd745c820b83616d89d5", - "report.html:md5,fbef08e1b6bf5b9adb5e8477e6c7d558", "TestMe.assembly.gfa.gz:md5,23a7fcda434d9d31bc77c88db004f2f8", "TestMe.scaffolds.fa.gz:md5,0f8a3007f245df1870c892ed11a60f94", - "TestMe-bacteria_odb10-busco.log:md5,b069f27f17602d7cfec21162ff780f74", - "predicted.faa:md5,bbbbea291ac723641fd0dac2622c4ad6", - "predicted.fna:md5,bcb2e8c5028d58cd02bbbef48c9b32ff", - "prodigal_mode_single_code_11.faa:md5,37cb1a2b36590d9797a34f1af768a6b2", - "prodigal_mode_single_code_11.fna:md5,4e524996faba75f510066538561945b6", - "prodigal_mode_single_code_4.faa:md5,394b84f41dfac67320a86c5f1ef568ae", - "prodigal_mode_single_code_4.fna:md5,bcb2e8c5028d58cd02bbbef48c9b32ff", - "full_table.tsv:md5,ba268ac1e6e2932cf31da37b8718d4da", - "missing_busco_list.tsv:md5,87cd16a4ee15f96c3d5671ef39f6e417", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json:md5,4c394bc1555895c4721962882981c9b2", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt:md5,4c133639191fda2f69e8cb6557032bd8", - "mqc_busco_plot_bacteria_odb10_1.yaml:md5,f4a956664f60d63198a7d2e006919e95", "mqc_nanostat_quality_dist_1.yaml:md5,56c27ab1c9f26bd454e5db00f1c3d573", "mqc_porechop-endtrim-barplot_1.yaml:md5,01be4aa5df6783634f6e8bb8208f550d", "mqc_porechop-middlesplit-barplot_1.yaml:md5,d7c6c6307fa5a50527bd1aa179c0dab5", "mqc_porechop-starttrim-barplot_1.yaml:md5,af425e12dc2f12ca3a611f24ec8cd5b7", - "mqc_prokka_plot_1.yaml:md5,7608a182fb8bcf98de3ced5a735af47c", - "mqc_quast_num_contigs_1.yaml:md5,aeb770bd1b8e8136a686ffb49a44c2fe", - "multiqc_busco.yaml:md5,f1b72e7b15508572a622adb37acd7d6f", "multiqc_citations.yaml:md5,80450f20190a42871cb64f62ae9bec3e", - "multiqc_general_stats.yaml:md5,294351007a56c8361d56eda4ebad5be2", - "multiqc_nanostat.yaml:md5,044869a9bdb292fbbd0e5a285739aa53", - "multiqc_prokka.yaml:md5,0223829d085a98e6819241380e8f2ae9", - "multiqc_quast.yaml:md5,696a51d7f09aafbf1632cee2821c8bc3", - "porechop.yaml:md5,403a3ef2261ef90756f67fc78b4ce556", - "TestMe.porechop.log:md5,b1c238975cd7e3f36a08b23a623ec4f6" + "multiqc_nanostat.yaml:md5,044869a9bdb292fbbd0e5a285739aa53" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T18:44:11.221082898" + "timestamp": "2025-07-08T08:50:25.380907714" } } \ No newline at end of file diff --git a/tests/long_dragonflye.nf.test b/tests/long_dragonflye.nf.test index 3752359e..09b75d18 100644 --- a/tests/long_dragonflye.nf.test +++ b/tests/long_dragonflye.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**','**/mqc_quast_num_contigs_1.yaml','**/multiqc_busco.yaml','**/multiqc_quast.yaml','**/mqc_busco_plot_*.yaml']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/long_dragonflye.nf.test.snap b/tests/long_dragonflye.nf.test.snap index 69b80c1c..37cfc3ae 100644 --- a/tests/long_dragonflye.nf.test.snap +++ b/tests/long_dragonflye.nf.test.snap @@ -58,7 +58,6 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250707_1844.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -71,20 +70,6 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/Channel_occupancy_of_the_flowcell.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/PHRED_score_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/Read_length_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/Yield_plot_through_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/images/plotly.min.js", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/report.data", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-184431/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -218,78 +203,18 @@ "trimming/longreads/porechop/TestMe.porechop.log" ], [ - "TestMe.dragonflye.log:md5,9597f9adbb4e6b4eea7c204ed385d852", - "TestMe.fa:md5,c7de28bdba39f097f23d4cf11f3c8193", - "TestMe_polished_genome.fa:md5,379b05e447dde6c80d23e96f16623b17", - "TestMe.faa:md5,23892a20a1a37af1ae4dd53f5a0d2f99", - "TestMe.ffn:md5,3f853e74afd258fdc52fe126584e7c02", - "TestMe.fna:md5,5ec2d47f89a394955de5cbb39ff8b84c", - "TestMe.fsa:md5,45b4caf94ca9d4ecaf9334ce4e7de59d", - "TestMe.gff:md5,9e0639d4fcdb05299669f8ebaca1a771", - "TestMe.tbl:md5,e9ce9eacb29869776e0c68ff05a2d27d", - "TestMe.tsv:md5,f0caecfdc0acba049acd75e22573912c", - "TestMe.txt:md5,e28d73997c3fc736c2463cf842e2ea26", - "LengthvsQualityScatterPlot_dot.html:md5,133000a3a0f5225b86219692cd4c7f58", - "LengthvsQualityScatterPlot_dot.png:md5,c2bc14fe29133fff3223ccedef9582c3", - "LengthvsQualityScatterPlot_kde.html:md5,a99de83f46e4e1dc8b2368aa3323bde2", - "LengthvsQualityScatterPlot_kde.png:md5,ad176488c291102d0e25870c71df4996", - "NanoPlot-report.html:md5,d602b85d05ad4fac2780679c6b152bad", - "NanoPlot_20250707_1844.log:md5,c0902bedc30368f52caa2ce27e45ceeb", - "Non_weightedHistogramReadlength.html:md5,304eb6f65ad3506086ad4694d7530d17", - "Non_weightedHistogramReadlength.png:md5,4a88af0963bea753816871ab2415c146", - "Non_weightedLogTransformed_HistogramReadlength.html:md5,7e42297684d86bbc12bf6652429eec55", - "Non_weightedLogTransformed_HistogramReadlength.png:md5,45cf40406afcd811446dee42e7bce6de", - "TestMe.txt:md5,07cbf8b60376bfec28d3dfdbadc7d0e9", - "WeightedHistogramReadlength.html:md5,2b48005d216582c8feab79c84d19a2ff", - "WeightedHistogramReadlength.png:md5,781f3c14ffd74744a7534e5b4d5135a1", - "WeightedLogTransformed_HistogramReadlength.html:md5,02691bf9609c3baa8d4801ffef71ba18", - "WeightedLogTransformed_HistogramReadlength.png:md5,206cc08d2f5e84dbd24300566c144c31", - "Yield_By_Length.html:md5,0f6fe9d62d77c06089b35aabee67a16b", - "Yield_By_Length.png:md5,887d78b1d94d67d5bd381cbc18d3e767", - "Channel_occupancy_of_the_flowcell.html:md5,b65d1243e299bf9857a913854fdb0bc5", - "Correlation_between_read_length_and_PHRED_score.html:md5,dcaa39cd74b08c2a2f2c3c6e004d8b1b", - "Distribution_of_read_lengths.html:md5,38fb636f45b98ac2b2a5794d13f13e2d", - "PHRED_score_density_distribution.html:md5,c71ac8920fec69918355ab19b3aa3edd", - "PHRED_score_distribution.html:md5,2161ffcb6785ecb64b67f5203e3abb72", - "PHRED_score_over_time.html:md5,7c4dfeb0c17a203a94d40188e451ce21", - "Read_count_histogram.html:md5,fe6216b6d760f490b4c5a57b7475c293", - "Read_length_over_time.html:md5,50507a65f73248324e1045c7a1b17120", - "Yield_plot_through_time.html:md5,f5ac802a3d10e4dbcdd518d4537b779e", - "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", - "report.data:md5,6170080965fff4e4480684cb3180d19c", - "report.html:md5,b9299af0ac0c64b70f68a1960f0b2712", - "TestMe-bacteria_odb10-busco.log:md5,014e523cf3ae06ac7d2830352f8e21aa", - "predicted.faa:md5,df008f814b23e9d104f031840f562caa", - "predicted.fna:md5,c61fd79fb81c25849179104c822c75e1", - "prodigal_mode_single_code_11.faa:md5,2d8da956b13ef0002209b066d5ef4472", - "prodigal_mode_single_code_11.fna:md5,0cc3ec48f79962873781f52bdbbec383", - "prodigal_mode_single_code_4.faa:md5,43ac632b4d5ed91eff82f450049f46e9", - "prodigal_mode_single_code_4.fna:md5,c61fd79fb81c25849179104c822c75e1", - "full_table.tsv:md5,bf620ddaab89b24405b8d2e99041725a", - "missing_busco_list.tsv:md5,e3ef2ca920366fb20bf9efca9b10bfee", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json:md5,9fecfba7c9356f85080567f0eebd183d", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt:md5,d4d12eb0443b357c1830695d509f0f83", - "mqc_busco_plot_bacteria_odb10_1.yaml:md5,4c8ff8d6dcacfae1d403cd092b6b0ecd", "mqc_nanostat_quality_dist_1.yaml:md5,56c27ab1c9f26bd454e5db00f1c3d573", "mqc_porechop-endtrim-barplot_1.yaml:md5,01be4aa5df6783634f6e8bb8208f550d", "mqc_porechop-middlesplit-barplot_1.yaml:md5,d7c6c6307fa5a50527bd1aa179c0dab5", "mqc_porechop-starttrim-barplot_1.yaml:md5,af425e12dc2f12ca3a611f24ec8cd5b7", - "mqc_prokka_plot_1.yaml:md5,411b709a811389621c325b221268c22b", - "mqc_quast_num_contigs_1.yaml:md5,c7a146b7ca0f31b42ed2dea91aca4932", - "multiqc_busco.yaml:md5,9ac92bf9a4137be2f4f5a879c5145c6d", "multiqc_citations.yaml:md5,80450f20190a42871cb64f62ae9bec3e", - "multiqc_general_stats.yaml:md5,e2cf0507f99b0a4c10fc258c97167ba7", - "multiqc_nanostat.yaml:md5,044869a9bdb292fbbd0e5a285739aa53", - "multiqc_prokka.yaml:md5,eae1ff1cb28f632e0b436c14b829c0ee", - "multiqc_quast.yaml:md5,b43db95a342a25f1ee15c4455ec17561", - "porechop.yaml:md5,403a3ef2261ef90756f67fc78b4ce556", - "TestMe.porechop.log:md5,17eafdb4136fa8b0b9d0b9533b6b20fc" + "multiqc_nanostat.yaml:md5,044869a9bdb292fbbd0e5a285739aa53" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T18:53:53.207499891" + "timestamp": "2025-07-08T10:26:53.741938295" } } \ No newline at end of file diff --git a/tests/long_liftoff.nf.test.snap b/tests/long_liftoff.nf.test.snap index 12962f22..abf475a0 100644 --- a/tests/long_liftoff.nf.test.snap +++ b/tests/long_liftoff.nf.test.snap @@ -341,24 +341,6 @@ "ERR044595.scaffolds.fa.gz:md5,5607023f2e453ce5da9f0a36780bba60", "ERR064912.assembly.gfa.gz:md5,d3ad512273883e85aab9ae52e07eb0b8", "ERR064912.scaffolds.fa.gz:md5,067f5be263d706a08b8d578e89d724d8", - "ERR044595-bacteria_odb10-busco.log:md5,477fae56e94108256805baed179c0fe8", - "predicted.faa:md5,9167f01c56cbb72cbe7fa4da6b3b3710", - "predicted.fna:md5,7ae7cced219e8575e3cca063961ad999", - "prodigal_mode_single_code_11.faa:md5,5e5298de767b28054112fafb2a0a3604", - "prodigal_mode_single_code_11.fna:md5,7ae7cced219e8575e3cca063961ad999", - "full_table.tsv:md5,0520030619f1fe037a612d87a9d508d9", - "missing_busco_list.tsv:md5,4cf87529bc0c6d1f3050e635653948dc", - "ERR064912-bacteria_odb10-busco.log:md5,7c0b43ca2024d20d40d6892f52be2f46", - "predicted.faa:md5,682b87bb8a8d677ed02ba2aa31fb07ff", - "predicted.fna:md5,7d21072bdfc82afeb7180e01a02b786f", - "prodigal_mode_single_code_11.faa:md5,bf97761e1b9bcac6f838a24d50de6c2f", - "prodigal_mode_single_code_11.fna:md5,7d21072bdfc82afeb7180e01a02b786f", - "full_table.tsv:md5,73afd7a0b817b1cd64ee71a6e4ea4bcd", - "missing_busco_list.tsv:md5,4cf87529bc0c6d1f3050e635653948dc", - "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.json:md5,46e8ca77109160a3ab05906d1e41012b", - "short_summary.specific.bacteria_odb10.ERR044595.scaffolds.fa.txt:md5,44f6f88969f89ed54513c4a2ea470dd4", - "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.json:md5,0c06526cfdb7e6f2a84208d57481bae4", - "short_summary.specific.bacteria_odb10.ERR064912.scaffolds.fa.txt:md5,03f9fe9fa7e39c684e3fa2939878289f", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,d095cfa297352d240023df5030592c44", "mqc_fastp-insert-size-plot_1.yaml:md5,502eb7cce116025829ba91041bd8e06f", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,1626ad6d4b0e5c11b812eb28f010bb30", @@ -390,14 +372,11 @@ "mqc_fastqc_sequence_duplication_levels_plot-2_1.yaml:md5,904ae9ce7abc638239879b6d16ff80a8", "mqc_fastqc_sequence_duplication_levels_plot_1.yaml:md5,4839cd6c3bd11763f6f58ec0c1fd75b2", "mqc_fastqc_sequence_length_distribution_plot_1.yaml:md5,2a0bfc0ec257081a52bf4f1755dd246b", - "mqc_quast_num_contigs_1.yaml:md5,98c3bbef635dac3f5afe78c1f6718e5e", "multiqc_busco.yaml:md5,003b890081970ec29305149c67f67cc9", "multiqc_citations.yaml:md5,e46f6ed003947fe967edd4674a82d4c6", "multiqc_fastp.yaml:md5,562cb7689bb8074a7bca26ae8a129996", "multiqc_fastqc.yaml:md5,05172556a25feb1277e789e91031d3bc", "multiqc_fastqc_1.yaml:md5,a4bc353bd4a67c1f480fb890d806bf6a", - "multiqc_general_stats.yaml:md5,c1a9086493cf9a79e03a29941dbddd85", - "multiqc_quast.yaml:md5,ae6477bf080e3c3cd57bef7a5e2e6255", "ERR044595.fastp.json:md5,ab69a1d8f62b6e1be76c83bb1022e882", "ERR064912.fastp.json:md5,b79afd61a88a0637d49b78537c2938e8" ] @@ -406,6 +385,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T19:15:59.829768165" + "timestamp": "2025-07-08T10:50:06.445977932" } } \ No newline at end of file diff --git a/tests/long_miniasm.nf.test b/tests/long_miniasm.nf.test index af4410a6..6882b0d2 100644 --- a/tests/long_miniasm.nf.test +++ b/tests/long_miniasm.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/long_miniasm.nf.test.snap b/tests/long_miniasm.nf.test.snap index 88ed5366..e457fb84 100644 --- a/tests/long_miniasm.nf.test.snap +++ b/tests/long_miniasm.nf.test.snap @@ -74,7 +74,6 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250707_1916.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -87,20 +86,6 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Channel_occupancy_of_the_flowcell.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/PHRED_score_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Read_length_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/Yield_plot_through_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/images/plotly.min.js", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/report.data", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-191635/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -296,55 +281,8 @@ "trimming/longreads/porechop/TestMe.porechop.log" ], [ - "TestMe_polished_genome.fa:md5,bee4dfb36cf899714c64c4c3b3cc117a", "TestMe.consensus.fasta.gz:md5,4899e7b112077d045ecaf13daae4ae4a", "TestMe.fasta.gz:md5,cfde74bc269a51162851d9ae7c76207b", - "TestMe.faa:md5,79febcef96cd36b51d0d6eab6e8271c0", - "TestMe.ffn:md5,5b1d7387b9757b1f7b33ca6f57f6e86f", - "TestMe.fna:md5,8010c63c334c529197a3b51dd7a12926", - "TestMe.fsa:md5,20c67cfc8e2a575a64aa6cd756dd4d96", - "TestMe.gff:md5,5a14fbe813225712b6ae97f7b0900a75", - "TestMe.tbl:md5,5e3209c87a4a5f8e560d61e0ac20abe0", - "TestMe.tsv:md5,ebc9ab98a77057557ce040a785af50fb", - "TestMe.txt:md5,d2f0c11aaac8fa90a1d207a80ca9713a", - "LengthvsQualityScatterPlot_dot.html:md5,e4d59802af8d97d3e835ac259068162b", - "LengthvsQualityScatterPlot_dot.png:md5,dcf143e4d6198159704b3fffd3d5d70c", - "LengthvsQualityScatterPlot_kde.html:md5,085402225fe03e9c54a2109a40ba43ce", - "LengthvsQualityScatterPlot_kde.png:md5,feb5018f0e9867b507ace39669ed8536", - "NanoPlot-report.html:md5,e8851222847ee3353280b66c69b3afad", - "NanoPlot_20250707_1916.log:md5,411738d2ac6c7c67531102d49daa5143", - "Non_weightedHistogramReadlength.html:md5,59abed6d5f4e55e1a323527c62ff8b49", - "Non_weightedHistogramReadlength.png:md5,4a88af0963bea753816871ab2415c146", - "Non_weightedLogTransformed_HistogramReadlength.html:md5,a39ecf2531c35ec0cfd0110592ddc4c1", - "Non_weightedLogTransformed_HistogramReadlength.png:md5,45cf40406afcd811446dee42e7bce6de", - "TestMe.txt:md5,07cbf8b60376bfec28d3dfdbadc7d0e9", - "WeightedHistogramReadlength.html:md5,307be843a25fca123da480e9643b53aa", - "WeightedHistogramReadlength.png:md5,781f3c14ffd74744a7534e5b4d5135a1", - "WeightedLogTransformed_HistogramReadlength.html:md5,77aff4eaa9ea74872c360fcbddaed4f5", - "WeightedLogTransformed_HistogramReadlength.png:md5,206cc08d2f5e84dbd24300566c144c31", - "Yield_By_Length.html:md5,542a0ddb1ddab3d1cc5bce6ac55cf08a", - "Yield_By_Length.png:md5,28a46b99f1a1b75a7558ae26da383716", - "Channel_occupancy_of_the_flowcell.html:md5,63275ed3c53ffac238d908b66b68cba0", - "Correlation_between_read_length_and_PHRED_score.html:md5,44128f802c7cf7050891eba172ad0d90", - "Distribution_of_read_lengths.html:md5,377373dfa65f36ec3f7c44b15a83eed5", - "PHRED_score_density_distribution.html:md5,943d024bc240fee5528f7b0418de7693", - "PHRED_score_distribution.html:md5,2548aeb7ed4c429472aa337ae59cd397", - "PHRED_score_over_time.html:md5,8b92393fd983d04952d729adfb84fa72", - "Read_count_histogram.html:md5,e1411b1d8f82a0dc435c36b59f5eb0a5", - "Read_length_over_time.html:md5,653b44250c1b3651cc81d728fc2ae02a", - "Yield_plot_through_time.html:md5,d410c7f89046d3a607425ca19e05bf8c", - "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", - "report.data:md5,98659348d30317c8a12245b16720d85a", - "report.html:md5,a533b238b5111c272671d9ae0d580af9", - "TestMe-bacteria_odb10-busco.log:md5,8d6c883ef6ffab8a936220cecef9d6f3", - "predicted.faa:md5,16a3aac79ea75a1e12247e7f7343efd5", - "predicted.fna:md5,43536c1a9728a2b42fd4d0e10d7b4905", - "prodigal_mode_single_code_11.faa:md5,ef2c29786ba66d49dfeadefbbeddb5bc", - "prodigal_mode_single_code_11.fna:md5,43536c1a9728a2b42fd4d0e10d7b4905", - "full_table.tsv:md5,8370ec39545e0013695452a08870921a", - "missing_busco_list.tsv:md5,feefc058b3c5a8d84b5cbd0e1dd66d14", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json:md5,72e56f717f7552647d5a51426a17e357", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt:md5,c46233ec2c5eb6344aed09ac3f742e33", "TestMe_longreads.txt:md5,4c2a95acdff03caa1524a5328c6ab2f5", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,20fcdbcf0d9962d242918c55db416b05", "mqc_kraken-top-n-plot_Class.yaml:md5,057a9ddcdb8a79e6c0fd5cfb0c0f94c9", @@ -360,23 +298,16 @@ "mqc_porechop-endtrim-barplot_1.yaml:md5,01be4aa5df6783634f6e8bb8208f550d", "mqc_porechop-middlesplit-barplot_1.yaml:md5,d7c6c6307fa5a50527bd1aa179c0dab5", "mqc_porechop-starttrim-barplot_1.yaml:md5,af425e12dc2f12ca3a611f24ec8cd5b7", - "mqc_prokka_plot_1.yaml:md5,ef610906b3c7fa15299db8cf80ebd057", - "mqc_quast_num_contigs_1.yaml:md5,d62597eba5fc5884e4c53b1a3e1f8ec8", "multiqc_busco.yaml:md5,226e0e15f4b333a589c94dc6f449c60b", "multiqc_citations.yaml:md5,683ec25d002e4678ebfdee6cfe8f1930", - "multiqc_general_stats.yaml:md5,11d974906541d4974dbe5440c48fd76e", "multiqc_kraken.yaml:md5,2579a276fcd6e51c35b361fd803d6d0b", - "multiqc_nanostat.yaml:md5,044869a9bdb292fbbd0e5a285739aa53", - "multiqc_prokka.yaml:md5,bdeb02de124bb0708aecd98dd8c7b04d", - "multiqc_quast.yaml:md5,8d1f429d20b60939e07454e334e03a06", - "porechop.yaml:md5,403a3ef2261ef90756f67fc78b4ce556", - "TestMe.porechop.log:md5,e83cf74f7feff1e991cbd374e6854787" + "multiqc_nanostat.yaml:md5,044869a9bdb292fbbd0e5a285739aa53" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T19:20:11.541894004" + "timestamp": "2025-07-08T10:53:47.019782537" } } \ No newline at end of file diff --git a/tests/long_miniasm_prokka.nf.test.snap b/tests/long_miniasm_prokka.nf.test.snap index df955d72..e5653f45 100644 --- a/tests/long_miniasm_prokka.nf.test.snap +++ b/tests/long_miniasm_prokka.nf.test.snap @@ -67,7 +67,7 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250707_1920.log", + "QC_longreads/NanoPlot/NanoPlot_20250708_1054.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -80,20 +80,20 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/Channel_occupancy_of_the_flowcell.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/PHRED_score_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/Read_length_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/Yield_plot_through_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/images/plotly.min.js", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/report.data", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-07-192031/report.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Channel_occupancy_of_the_flowcell.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Correlation_between_read_length_and_PHRED_score.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Distribution_of_read_lengths.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/PHRED_score_density_distribution.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/PHRED_score_distribution.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/PHRED_score_over_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Read_count_histogram.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Read_length_over_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Yield_plot_through_time.html", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/plotly.min.js", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/report.data", + "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -495,7 +495,6 @@ "trimming/longreads/porechop/TestMe.porechop.log" ], [ - "TestMe_polished_genome.fa:md5,7092cedd1cb6d0f185619755c5a2991d", "TestMe.consensus.fasta.gz:md5,199994f97a7c7617af79e334ae388a46", "TestMe.fasta.gz:md5,11ae7a338e60155a4c132bd2165339cd", "TestMe.faa:md5,61c3e89f58773111c3dab8eb8317350b", @@ -506,67 +505,20 @@ "TestMe.tbl:md5,eadad310078ad919e617701cb02a7784", "TestMe.tsv:md5,1e4b7c53f3ba35fa977c4693e278d30b", "TestMe.txt:md5,374388c4bf3d022b62d061bb494d4a53", - "LengthvsQualityScatterPlot_dot.html:md5,9df283908beb73ec4ee8f5e8bc388b92", - "LengthvsQualityScatterPlot_dot.png:md5,7510dd0637352d1185b75e97553f5cd1", - "LengthvsQualityScatterPlot_kde.html:md5,da6e1a0d517b2b769a7458a8774fb39a", - "LengthvsQualityScatterPlot_kde.png:md5,9481482afa55c99b76f3261b9b8efefc", - "NanoPlot-report.html:md5,e9ccc4860081c1c62cafd5c0ccf0fa9b", - "NanoPlot_20250707_1920.log:md5,3717680c447a4c03119730c2deaba660", - "Non_weightedHistogramReadlength.html:md5,cf919d795fd03c5e52d264603aec8c9e", - "Non_weightedHistogramReadlength.png:md5,251ad8aceb72f9905e06d5704f86e66c", - "Non_weightedLogTransformed_HistogramReadlength.html:md5,9e3700c529ead5dfdac586a37f726f56", - "Non_weightedLogTransformed_HistogramReadlength.png:md5,7a81280b5d06ec9fd8a3322edee55426", - "TestMe.txt:md5,9026fca74ef9bf4de88094c47ffe0c86", - "WeightedHistogramReadlength.html:md5,9cfac0d8c7cfd2ae3617afbfc24b0316", - "WeightedHistogramReadlength.png:md5,d7a3929470c4d538e2688b5b553e133f", - "WeightedLogTransformed_HistogramReadlength.html:md5,e5ff7d1244fe94152b25ab81d47ff12f", - "WeightedLogTransformed_HistogramReadlength.png:md5,96d5e46ee816c396f53b14ec414e3924", - "Yield_By_Length.html:md5,fe2e84d11e0bdd0aaa7d0bba1e96659b", - "Yield_By_Length.png:md5,0601420f5e008f9b297c0e74489cb8aa", - "Channel_occupancy_of_the_flowcell.html:md5,9df0630f5788e09db43a52cec9b267b7", - "Correlation_between_read_length_and_PHRED_score.html:md5,70657ad403bb1cf7dbaafc53572299a0", - "Distribution_of_read_lengths.html:md5,daccc8e68b8df2deaed9d2a8e05ec26f", - "PHRED_score_density_distribution.html:md5,991f94509d7a6438566ffab72f259666", - "PHRED_score_distribution.html:md5,3eb5adf82db7ec35a5f0a3b1dcbd3126", - "PHRED_score_over_time.html:md5,abd83ab40bebfb34f1e677c5d3096902", - "Read_count_histogram.html:md5,c10074d723ef1e51cf0b94aadb805183", - "Read_length_over_time.html:md5,f7cbdbf5d30295f6e0f662c534b01ed0", - "Yield_plot_through_time.html:md5,22d12b164293bb6b622f3d88365c7e5d", - "plotly.min.js:md5,059f6ecfa3930aa0b85b6ef4591390e4", - "report.data:md5,78d9d8e1a5073a6d3bc5e2825c2f55f6", - "report.html:md5,65d8e0a5e0e3e363424f0de9f30ee343", - "TestMe-bacteria_odb10-busco.log:md5,0304404e16ca1c5b524ce922039ff90c", - "predicted.faa:md5,d9d8ade611d7a2fc3dc3a26e50638ffa", - "predicted.fna:md5,0f499c98f12995a07285325de70e14c3", - "prodigal_mode_meta_code_11.faa:md5,e3c377dde8a3bb549aa8ee10a5012f5d", - "prodigal_mode_meta_code_11.fna:md5,0f499c98f12995a07285325de70e14c3", - "prodigal_mode_meta_code_4.faa:md5,e3c377dde8a3bb549aa8ee10a5012f5d", - "prodigal_mode_meta_code_4.fna:md5,0f499c98f12995a07285325de70e14c3", - "full_table.tsv:md5,0e7e88ec9a00f2911e5e2826a2c55d21", - "missing_busco_list.tsv:md5,ee72fcf3b896bca75487a26d348631a2", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json:md5,afd2a41ceef08d6dd1830c21261e6137", - "short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt:md5,2fde2d9e0ade56aebe033e47a179e7cd", "mqc_busco_plot_bacteria_odb10_1.yaml:md5,b0c60571185671c3a7a17280e257dee9", "mqc_nanostat_quality_dist_1.yaml:md5,4c825adfe187004dec6e2438f001c422", "mqc_porechop-endtrim-barplot_1.yaml:md5,711a2deae67088db22b1a2a462da4969", "mqc_porechop-middlesplit-barplot_1.yaml:md5,dab7cce19986f3193484fd241075b221", "mqc_porechop-starttrim-barplot_1.yaml:md5,d179142c064a1ab5d0d5eca777400982", - "mqc_prokka_plot_1.yaml:md5,fb6137b5f171620b3252ecc4a4687815", - "mqc_quast_num_contigs_1.yaml:md5,27fda5a380cac71274b9b6232f3d0a9a", "multiqc_busco.yaml:md5,c3eb539eb1f80483d02d72f7a7ec3844", "multiqc_citations.yaml:md5,80450f20190a42871cb64f62ae9bec3e", - "multiqc_general_stats.yaml:md5,4f99c61498841ec9ab898756d3c1e750", - "multiqc_nanostat.yaml:md5,199cc0d2dc4e425e371774b94ab38741", - "multiqc_prokka.yaml:md5,a2835805534e502fa4534c9e40a8aa5e", - "multiqc_quast.yaml:md5,4ac7024bfc6a590897231c9049bffed1", - "porechop.yaml:md5,02877aea8bb09d59145fc79a3c4f3115", - "TestMe.porechop.log:md5,ea7abbf36e95282491fc6f205aac64c7" + "multiqc_nanostat.yaml:md5,199cc0d2dc4e425e371774b94ab38741" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-07T19:22:07.100607554" + "timestamp": "2025-07-08T10:55:44.618168672" } } \ No newline at end of file From b03e004015794776e2cd7b1a40b5c14a7a0e47f9 Mon Sep 17 00:00:00 2001 From: d4straub Date: Tue, 8 Jul 2025 13:30:32 +0200 Subject: [PATCH 3/5] adjust also test_long_miniasm_prokka --- tests/long_miniasm_prokka.nf.test | 2 +- tests/long_miniasm_prokka.nf.test.snap | 285 +------------------------ 2 files changed, 2 insertions(+), 285 deletions(-) diff --git a/tests/long_miniasm_prokka.nf.test b/tests/long_miniasm_prokka.nf.test index 897b9cb9..ee2dc742 100644 --- a/tests/long_miniasm_prokka.nf.test +++ b/tests/long_miniasm_prokka.nf.test @@ -15,7 +15,7 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( diff --git a/tests/long_miniasm_prokka.nf.test.snap b/tests/long_miniasm_prokka.nf.test.snap index e5653f45..3e95d985 100644 --- a/tests/long_miniasm_prokka.nf.test.snap +++ b/tests/long_miniasm_prokka.nf.test.snap @@ -67,7 +67,6 @@ "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.html", "QC_longreads/NanoPlot/LengthvsQualityScatterPlot_kde.png", "QC_longreads/NanoPlot/NanoPlot-report.html", - "QC_longreads/NanoPlot/NanoPlot_20250708_1054.log", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.html", "QC_longreads/NanoPlot/Non_weightedHistogramReadlength.png", "QC_longreads/NanoPlot/Non_weightedLogTransformed_HistogramReadlength.html", @@ -80,20 +79,6 @@ "QC_longreads/NanoPlot/Yield_By_Length.html", "QC_longreads/NanoPlot/Yield_By_Length.png", "QC_longreads/ToulligQC", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Channel_occupancy_of_the_flowcell.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Correlation_between_read_length_and_PHRED_score.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Distribution_of_read_lengths.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/PHRED_score_density_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/PHRED_score_distribution.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/PHRED_score_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Read_count_histogram.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Read_length_over_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/Yield_plot_through_time.html", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/images/plotly.min.js", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/report.data", - "QC_longreads/ToulligQC/TestMeToulligqc-report-2025-07-08-105406/report.html", "QUAST", "QUAST/report", "QUAST/report/basic_stats", @@ -143,281 +128,13 @@ "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/.bbtools_output", "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/.bbtools_output/.checkpoint", "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/504464at2.faa", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/504464at2.fna", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences/multi_copy_busco_sequences", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences", "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/full_table.tsv", "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/.checkpoint", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1009041at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1024388at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1036075at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1043239at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1049662at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1054741at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1069591at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1074831at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1080436at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1093223at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1132353at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1151822at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1166299at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1211060at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1257362at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1266295at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1270636at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1272633at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1346419at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1395197at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1398618at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/1419877at2.out", - "busco/TestMe-bacteria_odb10-busco/TestMe_polished_genome.fa/run_bacteria_odb10/hmmer_output/143460at2.out", - 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"busco/busco_downloads/lineages/bacteria_odb10/hmms/1904463at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1906715at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1932144at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1937072at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1937493at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1940575at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1949059at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1959318at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1963491at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1971380at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1978865at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1990141at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/1990650at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2005443at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2012682at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2035880at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2040741at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2046660at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2063644at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2066663at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/2075502at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/219876at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/223233at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/226836at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/232152at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/26038at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/267682at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/353391at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/384865at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/402899at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/430176at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/4421at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/462069at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/469058at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/504464at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/505485at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/533698at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/662686at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/665824at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/761140at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/776861at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/837522at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/841869at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/874197at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/91428at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/923547at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/932854at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/932993at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/95696at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/9601at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/961486at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/981870at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/hmms/984717at2.hmm", - "busco/busco_downloads/lineages/bacteria_odb10/info", - "busco/busco_downloads/lineages/bacteria_odb10/info/ogs.id.info", - "busco/busco_downloads/lineages/bacteria_odb10/info/species.info", - "busco/busco_downloads/lineages/bacteria_odb10/lengths_cutoff", - "busco/busco_downloads/lineages/bacteria_odb10/links_to_ODB10.txt", - "busco/busco_downloads/lineages/bacteria_odb10/refseq_db.faa.gz", - "busco/busco_downloads/lineages/bacteria_odb10/refseq_db.faa.gz.md5", - "busco/busco_downloads/lineages/bacteria_odb10/scores_cutoff", "busco/short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.json", "busco/short_summary.specific.bacteria_odb10.TestMe_polished_genome.fa.txt", "multiqc", @@ -519,6 +236,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.2" }, - "timestamp": "2025-07-08T10:55:44.618168672" + "timestamp": "2025-07-08T13:29:16.043443427" } } \ No newline at end of file From bbb06ae8d18e2a0e4539f08a31d56931ef4e06b9 Mon Sep 17 00:00:00 2001 From: d4straub Date: Tue, 8 Jul 2025 14:43:40 +0200 Subject: [PATCH 4/5] remove busco summaries from hybrid_dragonflye --- tests/hybrid_dragonflye.nf.test | 2 +- tests/hybrid_dragonflye.nf.test.snap | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/tests/hybrid_dragonflye.nf.test b/tests/hybrid_dragonflye.nf.test index 15874546..c7845c70 100644 --- a/tests/hybrid_dragonflye.nf.test +++ b/tests/hybrid_dragonflye.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignoreFile: 'tests/.nftignore_files_entirely') // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**','**/mqc_quast_num_contigs_1.yaml','**/multiqc_quast.yaml']) + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['Prokka/**','**/mqc_quast_num_contigs_1.yaml','**/multiqc_quast.yaml','**/multiqc_busco.yaml','**/mqc_busco_plot_*.yaml']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/hybrid_dragonflye.nf.test.snap b/tests/hybrid_dragonflye.nf.test.snap index a8352397..cac24b14 100644 --- a/tests/hybrid_dragonflye.nf.test.snap +++ b/tests/hybrid_dragonflye.nf.test.snap @@ -355,7 +355,6 @@ "trimming/shortreads/log/A1403KPN.fastp.log" ], [ - "mqc_busco_plot_bacteria_odb10_1.yaml:md5,f518abd2780ef768903dd5da62548fdb", "mqc_fastp-insert-size-plot_1.yaml:md5,57eb8863c4b8db578660ab66c341ab07", "mqc_fastp-seq-content-gc-plot_Read_1_After_filtering.yaml:md5,b44852244e0643016e4b83c6bd507ac3", "mqc_fastp-seq-content-gc-plot_Read_1_Before_filtering.yaml:md5,f1a231f0f1df726c86132da8866be0a8", @@ -390,7 +389,6 @@ "mqc_porechop-endtrim-barplot_1.yaml:md5,a6396edf17f4e4ed9954cda933af2b7b", "mqc_porechop-middlesplit-barplot_1.yaml:md5,5e89ca1f45fb6876b58ddbb20b86ea77", "mqc_porechop-starttrim-barplot_1.yaml:md5,34e8d91183bd582532ac654e8e287945", - "multiqc_busco.yaml:md5,b645040c8295ca4a3b63af126dc68633", "multiqc_citations.yaml:md5,c1962a840fe1cf1698fbdeb8953601ed", "multiqc_fastp.yaml:md5,ed975e259ac4db3e9c2ba4dcd618fc18", "multiqc_fastqc.yaml:md5,a0b5fd24bb745bb77511c1962086fcf0", From 6da9a7faa9801249118079d0e147c2c27bdc8e1a Mon Sep 17 00:00:00 2001 From: d4straub Date: Tue, 8 Jul 2025 14:45:21 +0200 Subject: [PATCH 5/5] update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 39e4a14f..efcfff14 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#225](https://github.com/nf-core/bacass/pull/225) add BUSCO nf-core module. - [#223](https://github.com/nf-core/bacass/pull/223) Add nf-core/filtlong module. - [#222](https://github.com/nf-core/bacass/pull/222) Reinstalled Dragonflye 1.1.2. -- [#195](https://github.com/nf-core/bacass/pull/195) Update nf-core/bacass to the new nf-core 3.2.0 `TEMPLATE`. +- [#195](https://github.com/nf-core/bacass/pull/195),[#252](https://github.com/nf-core/bacass/pull/252) Update nf-core/bacass to the new nf-core 3.2.0 `TEMPLATE` and added nf-test ### `Fixed`