From 45cfed6eab818a6d820931fa97f5f66876325c87 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 8 Aug 2024 11:45:50 -0500 Subject: [PATCH] test: Update expected paths --- workflows/tests/aligner/bwa.nf.test | 50 +++++----- workflows/tests/aligner/bwa.nf.test.snap | 118 +++++++++++++++++++++-- 2 files changed, 138 insertions(+), 30 deletions(-) diff --git a/workflows/tests/aligner/bwa.nf.test b/workflows/tests/aligner/bwa.nf.test index 9c2c79ca..d5c9cd3d 100644 --- a/workflows/tests/aligner/bwa.nf.test +++ b/workflows/tests/aligner/bwa.nf.test @@ -21,28 +21,34 @@ nextflow_pipeline { { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") }, { assert snapshot( workflow.trace.tasks().size(), - path("$outputDir/bbmap").list(), - // BUG https://github.com/nf-core/nascent/issues/102 - // path("$outputDir/bedtools").list(), - // FIXME gtf2bed isn't deterministic - // path("$outputDir/bwa/featurecounts/gene").list(), - // FIXME cd4 isn't deterministic - // path("$outputDir/bwa/featurecounts/predicted").list(), - // path("$outputDir/deeptools").list(), - // path("$outputDir/fastp/*.json").list(), - // FIXME gtf2bed isn't deterministic - // path("$outputDir/gtf2bed").list(), - path("$outputDir/homer/cd4.bed"), - path("$outputDir/homer/jurkat.bed"), - // FIXME https://github.com/nf-core/nascent/issues/148 - // path("$outputDir/preseq").list(), - // path("$outputDir/rseqc").list(), - bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(), - bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(), - bam("$outputDir/samtools/cd4_REP3.sorted.bam").getSamLinesMD5(), - bam("$outputDir/samtools/cd4_REP4.sorted.bam").getSamLinesMD5(), - bam("$outputDir/samtools/jurkat_REP1.sorted.bam").getSamLinesMD5(), - bam("$outputDir/samtools/jurkat_REP2.sorted.bam").getSamLinesMD5(), + // TODO path("$outputDir/preprocessing/fastp/*.json").list(), + path("$outputDir/bwa/log").list(), + path("$outputDir/bwa/samtools_stats").list(), + path("$outputDir/quality_control/bbsplit").list(), + // FIXME Empty + path("$outputDir/quality_control/preseq").list().findAll { it.contains(".txt") }, + // process.out.outs[0][1].findAll { file(it).name.contains('.pb') }, + path("$outputDir/quality_control/rseqc/read_duplication/xls").list(), + path("$outputDir/quality_control/rseqc/read_duplication/rscript").list(), + path("$outputDir/quality_control/rseqc/infer_experiment").list(), + path("$outputDir/quality_control/rseqc/read_distribution").list(), + path("$outputDir/coverage_graphs/").list(), + // FIXME Empty + path("$outputDir/transcript_identification/").list().findAll { file(it.toString()).name.contains('.bed') }, + path("$outputDir/transcript_identification/homer/cd4.bed"), + path("$outputDir/transcript_identification/homer/jurkat.bed"), + // FIXME path("$outputDir/transcript_identification/pints/").list().findAll(), + path("$outputDir/transcript_identification/intersect/").list(), + path("$outputDir/transcript_identification/filtered/").list(), + // FIXME path("$outputDir/quantification/").list(), + path("$outputDir/multiqc/multiqc_report.html").exists(), + // TODO + // bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(), + // bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(), + // bam("$outputDir/samtools/cd4_REP3.sorted.bam").getSamLinesMD5(), + // bam("$outputDir/samtools/cd4_REP4.sorted.bam").getSamLinesMD5(), + // bam("$outputDir/samtools/jurkat_REP1.sorted.bam").getSamLinesMD5(), + // bam("$outputDir/samtools/jurkat_REP2.sorted.bam").getSamLinesMD5(), ).match("output_files") } ) diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap index 084b00e4..91b38b5d 100644 --- a/workflows/tests/aligner/bwa.nf.test.snap +++ b/workflows/tests/aligner/bwa.nf.test.snap @@ -2,6 +2,29 @@ "output_files": { "content": [ 134, + [ + + ], + [ + "cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906", + "cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2", + "cd4_REP1.sorted.bam.stats:md5,ba177ae2d9a5ab5a972bc056df28acc1", + "cd4_REP2.sorted.bam.flagstat:md5,0fd86dbf8f799fad49ba471702979bdc", + "cd4_REP2.sorted.bam.idxstats:md5,53204e4c6a9f68664087e4a8123be46a", + "cd4_REP2.sorted.bam.stats:md5,8c8fc51169528132b1cca54d3689e3c0", + "cd4_REP3.sorted.bam.flagstat:md5,793c9cadbf80e35dbae3774e9b5bd93f", + "cd4_REP3.sorted.bam.idxstats:md5,42de227ff397013cf288759871b0e938", + "cd4_REP3.sorted.bam.stats:md5,fe5be813bf2d55fd0e4877c650a0b266", + "cd4_REP4.sorted.bam.flagstat:md5,ed6c609505097f3cc9d9902d69e016f8", + "cd4_REP4.sorted.bam.idxstats:md5,959dc185ae59de4cebe374026711a55e", + "cd4_REP4.sorted.bam.stats:md5,46bf6f2b140d369986027bc2f588b440", + "jurkat_REP1.sorted.bam.flagstat:md5,fd5f02b0f02a407447b804b1d80f5421", + "jurkat_REP1.sorted.bam.idxstats:md5,c61af0847c1ad76c06a8de2815975b32", + "jurkat_REP1.sorted.bam.stats:md5,3f1b0a4214daa368a307f856f7a809dc", + "jurkat_REP2.sorted.bam.flagstat:md5,86ed47bd41a745ab59de473082c7742d", + "jurkat_REP2.sorted.bam.idxstats:md5,3db8f88c1f836eb5d10f37ca1df81ae9", + "jurkat_REP2.sorted.bam.stats:md5,48732cff30d5a9a272f68fc850b0eb84" + ], [ "cd4_REP1.coverage.hist.txt:md5,7cbb473be8d3b32ff2e52fdf4e5d10d2", "cd4_REP1.coverage.stats.txt:md5,f1471b61ac17dba283d80e08450c7e55", @@ -15,21 +38,100 @@ "jurkat_REP1.coverage.stats.txt:md5,381c69a30099d82066a959deab1a2569", "jurkat_REP2.coverage.hist.txt:md5,d124bdadaf2dc5cdd9e3db5a1ab4c588", "jurkat_REP2.coverage.stats.txt:md5,b1940346719e4070091f2eef6e508f49" + ], + [ + + ], + [ + "cd4_REP1.pos.DupRate.xls:md5,a80db2d20096ca839a7847ec5b11bf75", + "cd4_REP1.seq.DupRate.xls:md5,c34531fd7578c6f62cbad53b96a7feb9", + "cd4_REP2.pos.DupRate.xls:md5,06200ab67a60bee71fd168de88c15369", + "cd4_REP2.seq.DupRate.xls:md5,c82f6d687eacabbab045db34647c3254", + "cd4_REP3.pos.DupRate.xls:md5,fd3e91bfe070deccef65b265957cb733", + "cd4_REP3.seq.DupRate.xls:md5,f4c9f61081e6ef309abe82bb34aa4bd0", + "cd4_REP4.pos.DupRate.xls:md5,7fb8a7e96fd521561f62ccf7bf490212", + "cd4_REP4.seq.DupRate.xls:md5,8c671e5b0029d396a666839029298828", + "jurkat_REP1.pos.DupRate.xls:md5,0721c91ab7c640b046689095047657f8", + "jurkat_REP1.seq.DupRate.xls:md5,aba941b1bf0e93f99e39bd507d1c02de", + "jurkat_REP2.pos.DupRate.xls:md5,253ec69be4f5322dc92f6cb3fb41f7e0", + "jurkat_REP2.seq.DupRate.xls:md5,c7c83a29e6dfd49ff17858fe83dc07c8" + ], + [ + "cd4_REP1.DupRate_plot.r:md5,a6f96b5b87a142dca2e09868deb8222b", + "cd4_REP2.DupRate_plot.r:md5,a0686d22ba07f33a627c1a106d442a03", + "cd4_REP3.DupRate_plot.r:md5,5b37293c52beaecc5980aa2b9bafd82c", + "cd4_REP4.DupRate_plot.r:md5,ffa0f611b7f86d36134f9d80c3e1c9de", + "jurkat_REP1.DupRate_plot.r:md5,8e4dc99cae73c94eda275aeee08a5390", + "jurkat_REP2.DupRate_plot.r:md5,3507444f5965ca98a448ab15659ba34f" + ], + [ + "cd4_REP1.infer_experiment.txt:md5,2d8f31fe48cfc1db9d4c46ba59c2c7f3", + "cd4_REP2.infer_experiment.txt:md5,70ac3bf0d0c50d644ab97e1698021e55", + "cd4_REP3.infer_experiment.txt:md5,b0157d081d0ba0c27b370915f13c8c8a", + "cd4_REP4.infer_experiment.txt:md5,37ec4ee4ed5f707f073be5a7d4c9acfb", + "jurkat_REP1.infer_experiment.txt:md5,3ec36bed252146eb9cdb68db30c1855e", + "jurkat_REP2.infer_experiment.txt:md5,cde67a32fc922fb61fe5c5ea4b0e5c92" + ], + [ + "cd4_REP1.read_distribution.txt:md5,1fcc6afbb63242818d446b877a832c3a", + "cd4_REP2.read_distribution.txt:md5,c2762d927c1c12d520ebee8160561189", + "cd4_REP3.read_distribution.txt:md5,2f05c4cc866b4f8068e02008cad20cb3", + "cd4_REP4.read_distribution.txt:md5,ececae7f535b4fd5606bf763fdba7a34", + "jurkat_REP1.read_distribution.txt:md5,6c02a757ed379a6c19f6855e38b5d909", + "jurkat_REP2.read_distribution.txt:md5,a5f8bed2cff9d780a31c3ce43e289d9e" + ], + [ + "cd4_REP1.dreg.bedGraph:md5,8948a8fa86d8f6d413b77983189ff56e", + "cd4_REP1.minus.bedGraph:md5,2a1c34f9d9ef9ff1b9da7874b9e3aaad", + "cd4_REP1.minus.bigWig:md5,5280319275c98dcce023779fa389884d", + "cd4_REP1.plus.bedGraph:md5,1509ec3a921e3109c5914e1bcef8cf33", + "cd4_REP1.plus.bigWig:md5,72ccab3173f2018a22a4b36841247ba2", + "cd4_REP2.dreg.bedGraph:md5,29f865a5668fae4a52a41589ac2b3179", + "cd4_REP2.minus.bedGraph:md5,c530bc34fa3ec7ac49e88ff65f9c2f92", + "cd4_REP2.minus.bigWig:md5,5e748c794e037f441741f7f409c8c5ad", + "cd4_REP2.plus.bedGraph:md5,a675141da2874ec08d91591e5ea8242b", + "cd4_REP2.plus.bigWig:md5,08674d52e9eeb08807c33ed3e4b3d504", + "cd4_REP3.dreg.bedGraph:md5,201e690c619ee231416b643740141588", + "cd4_REP3.minus.bedGraph:md5,1c44c165f663d08c869a013b78f051b0", + "cd4_REP3.minus.bigWig:md5,aa3f5e86c635e182f9173543751cfbfd", + "cd4_REP3.plus.bedGraph:md5,a475098ed14da6f3242c4cfdf3abb713", + "cd4_REP3.plus.bigWig:md5,b255ae7c47424c223c537d00ecc025b5", + "cd4_REP4.dreg.bedGraph:md5,dfcfce7df666c0e24a3d0d4e21447a0b", + "cd4_REP4.minus.bedGraph:md5,b7a3d3c822155dfd8052c67a330fd6d5", + "cd4_REP4.minus.bigWig:md5,fc61c62613dc0f74a65c32419aba8f76", + "cd4_REP4.plus.bedGraph:md5,5623367b681562a2567afc62a8da4151", + "cd4_REP4.plus.bigWig:md5,ed00ad7a22c49860debc86cfa7ffb457", + "jurkat_REP1.dreg.bedGraph:md5,c25a4fb095e9f7d6766a3ce33e08f7d8", + "jurkat_REP1.minus.bedGraph:md5,8d5d9a41df6eb6c56b1bfd3f39dc1fc6", + "jurkat_REP1.minus.bigWig:md5,d06c8015c996bf520fff17266fd01f84", + "jurkat_REP1.plus.bedGraph:md5,6ed63e5983edaa74fb3965676efdb674", + "jurkat_REP1.plus.bigWig:md5,7a02334f2c7300ffdb5a2253c0937390", + "jurkat_REP2.dreg.bedGraph:md5,aad861b6fd8d296fe6bb4bc82d5eeeed", + "jurkat_REP2.minus.bedGraph:md5,cd83486cb6bb71e6b6e31a69c94d0d85", + "jurkat_REP2.minus.bigWig:md5,686f719978de948f7045acc95f9d1c82", + "jurkat_REP2.plus.bedGraph:md5,569e8a25c9cf48d1ef953f3da77c48a1", + "jurkat_REP2.plus.bigWig:md5,cbe3fd38fe8f9508645bbfad83924212" + ], + [ + ], "cd4.bed:md5,ab94918610a560772fdbec591200295f", "jurkat.bed:md5,41908723fa423a78476feb2e7627a3a4", - "c529a16c839e85e119b98354f109352d", - "9e63b682af88fa902cf92b5c485845b1", - "2aa200bbbce374ec7dedb9b46ce4aae1", - "122274730dd5386e1b26c174df886a8b", - "c2adf5327ff6d4edda2fdad00c7cb9bf", - "63fea3b1e2e08e5f6fdf3f7ba0aa7818" + [ + "cd4_intersect.bed:md5,d41d8cd98f00b204e9800998ecf8427e", + "jurkat_intersect.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "cd4_filtered.bed:md5,22a41b0aef6da7f4fa0f0644cc60ef32", + "jurkat_filtered.bed:md5,a491231815327b0d0fab1885b8a8662e" + ], + true ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T08:58:17.037588077" + "timestamp": "2024-08-09T17:35:32.797123474" }, "Should work with gzipped references": { "content": [ @@ -49,7 +151,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-04T20:12:41.277553487" + "timestamp": "2024-08-09T13:24:17.114505802" }, "Should work with BWA Index": { "content": [