From 1a9d087dbf76b1c6faf43b4821f1baf94956bb0b Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Wed, 21 Feb 2024 09:45:58 -0500 Subject: [PATCH 1/2] fix sample names _ join + update bismark tests, snap --- tests/pipeline/bismark/main.nf.test | 168 +++++++++++---- tests/pipeline/bismark/main.nf.test.snap | 258 +++++++++++++++++------ workflows/methylseq.nf | 2 +- 3 files changed, 320 insertions(+), 108 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index 11483301..cad98d07 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -19,33 +19,53 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam"), path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() } ) } } @@ -82,29 +102,47 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark/alignments/Ecoli_10K_methylated_R1_bismark_bt2_pe.bam"), - path("$outputDir/bismark/alignments/SRR389222.merged_bismark_bt2.bam"), + path("$outputDir/bismark/alignments/SRR389222_sub1_bismark_bt2.bam"), + path("$outputDir/bismark/alignments/SRR389222_sub2_bismark_bt2.bam"), + path("$outputDir/bismark/alignments/SRR389222_sub3_bismark_bt2.bam"), path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222.merged_bismark_bt2.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_bismark_bt2.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_bismark_bt2.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_bismark_bt2.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222.merged_bismark_bt2.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_bismark_bt2.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_bismark_bt2.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_bismark_bt2.M-bias.txt"), path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222.merged_bismark_bt2.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_bismark_bt2.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_bismark_bt2.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_bismark_bt2.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222.merged_bismark_bt2_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_bismark_bt2_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_bismark_bt2_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_bismark_bt2_splitting_report.txt"), path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end_rrbs") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222.merged_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_bismark_bt2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark/reports/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222.merged_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub1_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub2_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub3_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() } ) } @@ -143,36 +181,59 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.CpG.cov.gz"), path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.GpC.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub1.NOMe.CpG.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.CpG.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.CpG.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub1.NOMe.GpC.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.GpC.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.GpC.cov.gz"), path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam"), path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_nomeseq") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end_nomeseq") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_nomeseq_software_versions") }, { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() } ) } } @@ -191,34 +252,55 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam"), path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"), path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("clip_r1") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("clip_r1") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("clip_r1_software_versions") }, { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() } ) } } + + } diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 00af9199..81456011 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,90 +1,159 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:26:20.577627445" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T06:54:47.661957839" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:32:15.519069167" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T22:39:38.051328252" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:29:19.538788605" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T21:22:39.186789551" }, "single_end_nomeseq": { "content": [ "Ecoli.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", "Ecoli.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", - "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", - "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", + "SRR389222_sub1.NOMe.CpG.cov.gz:md5,087f5da64b9ab087a0e22fa11536871e", + "SRR389222_sub2.NOMe.CpG.cov.gz:md5,016eabe6c88ef719d8edffbe13d1b2ce", + "SRR389222_sub3.NOMe.CpG.cov.gz:md5,85098361910f7398528dcbb0e46a7561", + "SRR389222_sub1.NOMe.GpC.cov.gz:md5,25211d7e44488baf6193f753a5095b2f", + "SRR389222_sub2.NOMe.GpC.cov.gz:md5,10837f6099f63dc4aae2895d821a582e", + "SRR389222_sub3.NOMe.GpC.cov.gz:md5,8005a9dad4d0f5562a3c7cf215a18908", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7", - "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam:md5,66b4244c9f75ee798a77b0a1e47214ea", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam:md5,79e4d27508ee03d74bf4c79d23d439fd", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam:md5,d627ec0448a0bba875895615b90beab6", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,ccf9537924fa4aa1db2f4462d2b9bc8e", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,c352886f5d59592bc679843548ca5eef", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,0a489f15a4d3bb11236a8acf38ba0984", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,ed28b3cce432eecfae73bc4a071ec4ee", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b06ce0084e54193ff8c9b9dd0ec9757b", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b865b7fb6e1225feeb6aef3372ef0b1d", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,1a6e4ec040df8d20ca5ea84abd8c2f66", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,da676db243dde9438471d8ea8aa79fa5", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,55eadffbe1d31538a88d2fd5b65fd6e7", [ "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", + "CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a10f4263bf7b9b1985b16ff3c1041240", + "CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,1b036ec35b09e0d3b748040381cb1fd5", + "CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,929b960ad908ec05687540b684106de0", "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", + "CHG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,87d488061e2d43db2060a37874c346cc", + "CHG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2013c67301066dde516bb950731fb04a", + "CHG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e4d5f53c056424471038f28ffd49b2df", "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", + "CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,172b329b6aabf8d07c8255a152d4105a", + "CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,82e84337d3a4c5ca20260e7455c53022", + "CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d06408d5bb2071ae66a4d4260a73c491", "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", + "CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,20038a010d4258a2a76aa389e05b84ba", + "CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e585363a40c045ea66c16257e507d3de", + "CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9b529b04d321e5fc11dcb023345fd136", "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - 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"CHH_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", + "CHH_OB_SRR389222_sub1_bismark_bt2.txt.gz:md5,ddedeb6dcd4cc268d3db74e040fe21c3", + "CHH_OB_SRR389222_sub2_bismark_bt2.txt.gz:md5,d5ef03e73bd476a45d0c8ed2b50285bc", + "CHH_OB_SRR389222_sub3_bismark_bt2.txt.gz:md5,9909b6c627e4b520d623ece853806233", "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,2a356ae7fe7774f140f11ed5d935f88c", + "CHH_OT_SRR389222_sub1_bismark_bt2.txt.gz:md5,ba3e403fcd8020b65bd0eb320800fe54", + "CHH_OT_SRR389222_sub2_bismark_bt2.txt.gz:md5,cfd6e3af7c5923ad8133cc41cd8a0aec", + "CHH_OT_SRR389222_sub3_bismark_bt2.txt.gz:md5,0ce32443b301a0b8565f84aad2741af1", "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - "CpG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", + "CpG_OB_SRR389222_sub1_bismark_bt2.txt.gz:md5,2c91088668e203cf09eb2f6708dedb4e", + "CpG_OB_SRR389222_sub2_bismark_bt2.txt.gz:md5,887ce918c095bf35c31e1668dd54472d", + "CpG_OB_SRR389222_sub3_bismark_bt2.txt.gz:md5,0892e2fc97607fd2456343ff6b11fa4b", "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,9e517e44422a8bb22de1281ff2cd34d1" + "CpG_OT_SRR389222_sub1_bismark_bt2.txt.gz:md5,a96288b9ecdacbfe82c8e5ae99580a41", + "CpG_OT_SRR389222_sub2_bismark_bt2.txt.gz:md5,373632783251041aa761ad655bc177b6", + "CpG_OT_SRR389222_sub3_bismark_bt2.txt.gz:md5,3ae5766509809de3f8d411ad61cd1afa" ], "Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt:md5,fa089f6146df9667862970b6ddc998b0", - "SRR389222.merged_bismark_bt2_splitting_report.txt:md5,0ece57f8fc3aa659d2f0b7a09cf48398", + "SRR389222_sub1_bismark_bt2_splitting_report.txt:md5,f59eac7a30ec7f1f690aac921a5591c0", + "SRR389222_sub2_bismark_bt2_splitting_report.txt:md5,e4050820625d7d5b3ce82cb2dccc30ea", + "SRR389222_sub3_bismark_bt2_splitting_report.txt:md5,44122ee8a6a465c2714f28a38a97b5d0", [ [ [ @@ -163,40 +260,73 @@ "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" ], "genome_results.txt:md5,97dc2b4df61a46ccd2714903186ecaf0", - "genome_results.txt:md5,f0d293867800a75becf2583c23729083" + "genome_results.txt:md5,7a86634fd1c768d8302e071088641815", + "genome_results.txt:md5,b430f7924a342f3b4f6b9d71174943c0", + "genome_results.txt:md5,3610180287e00094e5399a5a13bda7ea" ], - "timestamp": "2023-12-22T22:52:42.829793102" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T21:22:37.920449641" }, "clip_r1": { "content": [ "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,b19bc9b84dd8d8000c05b04234689aca", - "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,1bfe463dabf8727992e3ff6c19d8e7c1", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam:md5,a247e14e142b818bad48322854802396", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam:md5,c0c7051ac9f63d6662b63d3b3cc44a2e", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam:md5,80e2dd817c0a04d060c92ab556865b3e", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,f662ef520f5e483cd6f2a4925afe2283", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,330d25130120699a9ca4cf7152f9ac18", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,9cd7348188fb06c7648b1453db5270c9", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", - "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,90a6b76d41112c6de391d3a017638d95", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,aab193316d15edf54271f7d3270ae963", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,81a0d0749e3df600572188afec21a9e3", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,818aaadc83209032dc234717455ae91d", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,51f024d22277e740f07b6fca27b2b159", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,beb2a4e9ef24ad73aa6807ddd17899d7", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,167ae8eabdeb46a3322f549f3b7c1285", [ "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", + "CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,31b39e298bf795c789e3d89bb709bb98", + "CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,34a16beb7ac6d65d6709414cbff27498", + "CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f42600e91af5f41713c9a55f13450829", "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c1ba1891636a6b99f4d1495b3ddf1a59", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f8867c4ee03fba6be823b7287cacfea3", + "CHG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,5124d5b168179d99ff67b8d4c100360b", + "CHG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e2f22012541680a83548def74eaba514", + "CHG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6d5d16424d66321e50529648d5116a16", "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,4e9a0e61d47eefb64876431b3640ee95", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,32728cf447a470681f4e608008d514ae", + "CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f5864218b65b694a408532a644b38a07", + "CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2ec16daaf1b54339fe8ea9ce82894a37", + "CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,8b9b10e41f0fea4e520f4aef9386c035", "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,10cd51608191667e027a9867dd84ab3f", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2ec291cbfc4d64dbcd50603839129de1", + "CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,309c4e519af35883e079c4edc2de9362", + "CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,80781dcc708f5f4d6db10ec32c2a6235", + "CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,aa21ac514f3959b20fc1e2f684b86df6", "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,423aa4faf47d176a6b6cce134e1a9212", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,873612f00ee6ef44e8bc0dcb9f4a35f6", + "CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e9359f258720294c9048c1fb411c884e", + "CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,85e322f6f76e9b5bcba21e6cec5250fb", + "CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,7b688d69cf15f16e1b7a84dad0e79b90", "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" + "CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9acb5d1553fa5fda822a34dc6e5a9b1c", + "CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,ec6963fc9e3fe3b98df339f0bd54c8db", + "CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a68b0dd668b12759d18c8e0feda70bc7" ], "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,db55b5dbf35e78de9c1c6b2f2ed1e45b", - "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,9a1a5d1e6722dda9e8a1953a01c415d0", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,4d719525ed5b4ca933ff681b955a0e20", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,545b7a29971239cdb3b4e620e8340640", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,fd6258e8c9af3d598a3648af8bd3067e", "genome_results.txt:md5,2bbc428b0a5b9828df9fc4cd92806e12", - "genome_results.txt:md5,5631f1632df00985946641cfc1601633" + "genome_results.txt:md5,5262b7434c519952b44e00258798eb9d", + "genome_results.txt:md5,0d44b70d9120e8e50591901dccee2871", + "genome_results.txt:md5,5508ce90851b844946f4c1a5395c2b14" ], - "timestamp": "2023-12-22T22:57:38.05813974" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T22:56:06.845565652" } } \ No newline at end of file diff --git a/workflows/methylseq.nf b/workflows/methylseq.nf index b49d895d..ac791108 100644 --- a/workflows/methylseq.nf +++ b/workflows/methylseq.nf @@ -100,7 +100,7 @@ workflow METHYLSEQ { meta, fastq -> def meta_clone = meta.clone() parts = meta_clone.id.split('_') - meta_clone.id = parts.length > 1 ? parts[0..-2].join('_') : meta_clone.id + meta_clone.id = parts.length > 1 ? parts.join('_') : meta_clone.id [ meta_clone, fastq ] } .groupTuple(by: [0]) From 457f9d64e47c48a892e6791ea6e058a022a03dc3 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Wed, 21 Feb 2024 23:00:31 -0500 Subject: [PATCH 2/2] update bismark_hisat2 & bwameth tests and snap --- tests/pipeline/bismark_hisat/main.nf.test | 78 ++++++++--- .../pipeline/bismark_hisat/main.nf.test.snap | 126 +++++++++++++----- tests/pipeline/bwameth/main.nf.test | 66 ++++++--- tests/pipeline/bwameth/main.nf.test.snap | 78 ++++++++--- 4 files changed, 257 insertions(+), 91 deletions(-) diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index 550fb843..b894d746 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -19,33 +19,52 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam"), - path("$outputDir/bismark_hisat/deduplicated/SRR389222_trimmed_bismark_hisat2.deduplicated.bam"), + path("$outputDir/bismark_hisat/deduplicated/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bam"), + path("$outputDir/bismark_hisat/deduplicated/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bam"), + path("$outputDir/bismark_hisat/deduplicated/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bam"), path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_1_val_1_bismark_hisat2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_trimmed_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub1_trimmed_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark_hisat/reports/Ecoli_1_val_1_bismark_hisat2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/SRR389222_trimmed_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub1_trimmed_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub2_trimmed_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub3_trimmed_bismark_hisat2_SE_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() } ) } } @@ -82,29 +101,46 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark_hisat/alignments/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam"), - path("$outputDir/bismark_hisat/alignments/SRR389222.merged_bismark_hisat2.bam"), + path("$outputDir/bismark_hisat/alignments/SRR389222_sub1_bismark_hisat2.bam"), + path("$outputDir/bismark_hisat/alignments/SRR389222_sub2_bismark_hisat2.bam"), + path("$outputDir/bismark_hisat/alignments/SRR389222_sub3_bismark_hisat2.bam"), path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222.merged_bismark_hisat2.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub1_bismark_hisat2.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub2_bismark_hisat2.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_sub3_bismark_hisat2.bedGraph.gz"), path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222.merged_bismark_hisat2.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub1_bismark_hisat2.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub2_bismark_hisat2.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_sub3_bismark_hisat2.M-bias.txt"), path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222.merged_bismark_hisat2.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub1_bismark_hisat2.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub2_bismark_hisat2.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_sub3_bismark_hisat2.bismark.cov.gz"), path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222.merged_bismark_hisat2_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub1_bismark_hisat2_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub2_bismark_hisat2_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub3_bismark_hisat2_splitting_report.txt"), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end_rrbs") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222.merged_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub1_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub2_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_sub3_bismark_hisat2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/SRR389222.merged_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub1_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub2_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_sub3_bismark_hisat2_SE_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() } ) } diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index 7386470f..13539740 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,78 +1,140 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:10:20.303057192" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:13:40.665667172" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:23:14.860048797" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:16:45.610326834" }, "single_end": { "content": [ "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,ddfc84eb92f641020362f69e9e28a52d", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bam:md5,aa60cf9dcf302c185b12ced6f302a06e", + "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bam:md5,0735542dc09bf837836158a1eae69828", + "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bam:md5,d777052608cf019a801e5748e5a71dcd", + "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bam:md5,27601bff15578ae06ef871d6821ce030", "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,b20f17236ff64db1114343ff333a6d5b", + "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,47f60a641b8564c14a0f08599215944b", + "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,2b5a22fd9d8bf25b993a8c0ad7beb13d", + "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,d42e09af121ae14f6e0de5779e317b0b", "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", - "SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,b19356395d4ae1ad83bd3ec38276e580", + "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,de08bb32cf22e361f9ca05058b4a5088", + "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,73808d508bff5a44a5ec956df0fc3f69", + "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,fee56ba84eecef9cf4ad8e01cdf1da87", [ "CHG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", - "CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", + "CHG_OB_SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,a10f4263bf7b9b1985b16ff3c1041240", + "CHG_OB_SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1b036ec35b09e0d3b748040381cb1fd5", + "CHG_OB_SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,929b960ad908ec05687540b684106de0", "CHG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1180631ef093aade3a5195ce7ddfb3f6", + "CHG_OT_SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,632b163026c8134e5e5cba1f32aef712", + "CHG_OT_SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,75214e5d9bc9b9116fa5573937c29d37", + "CHG_OT_SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,5a78c25cb94dc40876a5fee5c76e38a6", "CHH_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", - "CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", + "CHH_OB_SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,172b329b6aabf8d07c8255a152d4105a", + "CHH_OB_SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,82e84337d3a4c5ca20260e7455c53022", + "CHH_OB_SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,d06408d5bb2071ae66a4d4260a73c491", "CHH_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,c311a70c0c8b6a93c2055fcbec03a833", + "CHH_OT_SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,b19d5d318db483a8efce4af2fc5adadf", + "CHH_OT_SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,0a0c7eb15fac8f39933c05a66a1eb062", + "CHH_OT_SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,870d67a239d68537da5f98c38cde2adf", "CpG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", - "CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", + "CpG_OB_SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,d581258ecd66c080c70caeea30e31ca2", + "CpG_OB_SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,dee4913db39eef1e706167d6c0f0c389", + "CpG_OB_SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,74a9c8092dbd8c2f27d54bb627993f90", "CpG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,63e737eef999e2d6348e7ed2a7ce4402" + "CpG_OT_SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,f754de10c01ca07836f3058b637d3f1d", + "CpG_OT_SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,e3a4e5f59a783786df6effe5174692e7", + "CpG_OT_SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,23ac4420915aa61bd743210d9cc31ef0" ], "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ad7a19cb9908844c47b7b871ff1223c2", + "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,8f77dc7c0dea9e0c413e6a8c4fe3c9af", + "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,0da5af753da0274f3e6b66b04a11e73a", + "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,43f8554a2d19d172c16636374bb83084", "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,bc2284d712455231a2dd772098ca8dd9", - "SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,1f792e1fddb17140947f14008e1f9ffd", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,4020063dd8610b58b7b39c3ca62cef17", + "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,99b3eea4648b3156ca4b34972fe134e2", + "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,b2db30ce6a406ccb8cb05bfe7afd2d92", "genome_results.txt:md5,3703ab8cc04a6f3307ea1ffcfe23479a", - "genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f" + "genome_results.txt:md5,9956ed1dcf51e6975f4a6ab8fe156aba", + "genome_results.txt:md5,b96969ec83d32328c1948c9a11a70ad8", + "genome_results.txt:md5,0950f0f4bb7fe3b64b120da8d43c227b" ], - "timestamp": "2023-12-22T22:14:39.589478621" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:13:40.502832937" }, "single_end_rrbs": { "content": [ "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam:md5,53c34edee0bc7f34c9f4e9a3685dd706", - "SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb", + "SRR389222_sub1_bismark_hisat2.bam:md5,0964e2b21013062957755b9bcb71f804", + "SRR389222_sub2_bismark_hisat2.bam:md5,9a6b9476a76e37a73deb3f356fa97bc0", + "SRR389222_sub3_bismark_hisat2.bam:md5,01eacf366af88ad627c5c2262c2e4c3f", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", - "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", + "SRR389222_sub1_bismark_hisat2.bedGraph.gz:md5,75be0d8be0134a48fd55e15a49568d3f", + "SRR389222_sub2_bismark_hisat2.bedGraph.gz:md5,16e440f735d6506e4076b295bf3c953c", + "SRR389222_sub3_bismark_hisat2.bedGraph.gz:md5,fba953da8e5268150b3fe78ca6b8c31c", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", - "SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9", + "SRR389222_sub1_bismark_hisat2.M-bias.txt:md5,bbfe49763c571a55a50d1e46c0fb4e46", + "SRR389222_sub2_bismark_hisat2.M-bias.txt:md5,dfce7ce78360347d3f12734f99ba0047", + "SRR389222_sub3_bismark_hisat2.M-bias.txt:md5,6c4dcfe0bceb316c2f90ec0f39f0437f", [ "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", - "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", + "CHG_OB_SRR389222_sub1_bismark_hisat2.txt.gz:md5,c8ccffe89627f497f9b542400c9db8c2", + "CHG_OB_SRR389222_sub2_bismark_hisat2.txt.gz:md5,d845eb88cc123a6049020ab7c1f0be28", + "CHG_OB_SRR389222_sub3_bismark_hisat2.txt.gz:md5,06e38fdf5846663bc46b2c47d057a117", "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,7add3136b9f74de6aa83d38dde191060", + "CHG_OT_SRR389222_sub1_bismark_hisat2.txt.gz:md5,3d00f805423c9e0710648c059157c832", + "CHG_OT_SRR389222_sub2_bismark_hisat2.txt.gz:md5,f2e8c0b1e1b51f410a174189b53526a5", + "CHG_OT_SRR389222_sub3_bismark_hisat2.txt.gz:md5,71a81bc27e3df0597553488119f50622", "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", - "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", + "CHH_OB_SRR389222_sub1_bismark_hisat2.txt.gz:md5,ddedeb6dcd4cc268d3db74e040fe21c3", + "CHH_OB_SRR389222_sub2_bismark_hisat2.txt.gz:md5,d5ef03e73bd476a45d0c8ed2b50285bc", + "CHH_OB_SRR389222_sub3_bismark_hisat2.txt.gz:md5,9909b6c627e4b520d623ece853806233", "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,8f1910f962b724592546a6187ad0a677", + "CHH_OT_SRR389222_sub1_bismark_hisat2.txt.gz:md5,85131a52ee28f5a87ddbd0a6a2ab1618", + "CHH_OT_SRR389222_sub2_bismark_hisat2.txt.gz:md5,0d7fec9b1c6e3cba2a22cb607d59da98", + "CHH_OT_SRR389222_sub3_bismark_hisat2.txt.gz:md5,2c7cf34d4a6255818062d472e0effa13", "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", - "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", + "CpG_OB_SRR389222_sub1_bismark_hisat2.txt.gz:md5,2c91088668e203cf09eb2f6708dedb4e", + "CpG_OB_SRR389222_sub2_bismark_hisat2.txt.gz:md5,887ce918c095bf35c31e1668dd54472d", + "CpG_OB_SRR389222_sub3_bismark_hisat2.txt.gz:md5,0892e2fc97607fd2456343ff6b11fa4b", "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" + "CpG_OT_SRR389222_sub1_bismark_hisat2.txt.gz:md5,481c325285ccbfddd43cd04615c7e4bb", + "CpG_OT_SRR389222_sub2_bismark_hisat2.txt.gz:md5,77b0cacbc8a8f0997aae5314931e4907", + "CpG_OT_SRR389222_sub3_bismark_hisat2.txt.gz:md5,7323bac81ce1f763cfa00ebb70869794" ], "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", - "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", + "SRR389222_sub1_bismark_hisat2.bismark.cov.gz:md5,ab610e006112a52e5ecb230a1704f236", + "SRR389222_sub2_bismark_hisat2.bismark.cov.gz:md5,f8ac4bc2e000069f0daa22446a5bd899", + "SRR389222_sub3_bismark_hisat2.bismark.cov.gz:md5,05b5ca7f758f6be7346509cd5615ca05", "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765", - "SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "SRR389222_sub1_bismark_hisat2_splitting_report.txt:md5,754ed7bf4d75acee466c48c05a11d331", + "SRR389222_sub2_bismark_hisat2_splitting_report.txt:md5,45dc01d29a16eb04d4421133c74c0d77", + "SRR389222_sub3_bismark_hisat2_splitting_report.txt:md5,28ac733f2f58289368b0bcad9ef163ea", "genome_results.txt:md5,58bf4e22f697120806f09b48d9ffdc9e", - "genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49" + "genome_results.txt:md5,58a2aeeb5eacca4c766bb23fee8f9013", + "genome_results.txt:md5,a69850fa38b907dd9d416d097d043b05", + "genome_results.txt:md5,99be975e957ea5ca013b3d4e97f35835" ], - "timestamp": "2023-12-22T22:37:54.382841284" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:16:44.459903681" } } \ No newline at end of file diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 1863371e..438a4fd1 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -21,29 +21,48 @@ nextflow_pipeline { { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"), path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.stats"), path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam"), path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam.bai"), - path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam"), - path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam.bai"), + path("$outputDir/bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam"), + path("$outputDir/bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai"), + path("$outputDir/bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam"), + path("$outputDir/bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai"), + path("$outputDir/bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam"), + path("$outputDir/bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai"), path("$outputDir/bwameth/reference_genome/").list(), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), path("$outputDir/methyldackel/Ecoli.markdup.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222.markdup.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222_sub2.markdup.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222_sub3.markdup.sorted_CpG.bedGraph"), path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"), - path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222_sub1.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222_sub2.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222_sub3.mbias.txt"), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end") }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, - { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222.markdup.sorted.MarkDuplicates.metrics.txt").exists() } + { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, + { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, + { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.MarkDuplicates.metrics.txt").exists() } ) } } @@ -83,19 +102,30 @@ nextflow_pipeline { { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"), path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.stats"), path("$outputDir/bwameth/reference_genome/").list(), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), path("$outputDir/methyldackel/Ecoli.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222_sub1.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222_sub2.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222_sub3.sorted_CpG.bedGraph"), path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"), - path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222_sub1.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222_sub2.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222_sub3.mbias.txt"), path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, + path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"), + path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end_rrbs") }, { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() } ) } diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 4e2e1958..b1a25a78 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,26 +1,42 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:35:11.787754038" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:52:02.102780846" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.7.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.7.0dev}}" ], - "timestamp": "2024-02-09T22:36:36.796510773" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:53:27.861098792" }, "single_end": { "content": [ "Ecoli.flagstat:md5,f520e87cc4050799a0dbed72909572ec", "Ecoli.stats:md5,c09155913e0164da9010a0840618cf1f", - "SRR389222.flagstat:md5,f5a2dd6c9532bbfb8fe78aad010d8737", - "SRR389222.stats:md5,cc81b8c56d038e437a99d9c04b61ce2d", + "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", + "SRR389222_sub1.stats:md5,047e5fc07dd5975b6fcba41f7e506ef1", + "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", + "SRR389222_sub2.stats:md5,145fa2837bbaa85e6daf29e85f57ee79", + "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", + "SRR389222_sub3.stats:md5,1ddf0b5edccc308e1bc90b9a1afa6ca6", "Ecoli.markdup.sorted.bam:md5,0d1c814b476521286a829dc64fc3490a", "Ecoli.markdup.sorted.bam.bai:md5,befef6ce0a34e2ce7f66c073d9bf4abd", - "SRR389222.markdup.sorted.bam:md5,46b5b49280efe5d5c5d1692092e8926f", - "SRR389222.markdup.sorted.bam.bai:md5,ad6cfa0344e1ba5b9057ea39f337b3d2", + "SRR389222_sub1.markdup.sorted.bam:md5,cf2fa2a8b4fed92e3a03afd8999926b4", + "SRR389222_sub1.markdup.sorted.bam.bai:md5,c95cb45c3f0a9a82bf78a7914b38ebaf", + "SRR389222_sub2.markdup.sorted.bam:md5,a482e5162b902af2e6f692cdd829686e", + "SRR389222_sub2.markdup.sorted.bam.bai:md5,fbe5ef44841a8b6028bdb7c14ae67e59", + "SRR389222_sub3.markdup.sorted.bam:md5,314bb45a56082caced5025f9316a6393", + "SRR389222_sub3.markdup.sorted.bam.bai:md5,d7d62a85aac95328011ba48c37f3cf1c", [ [ "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", @@ -32,22 +48,35 @@ "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" ] ], - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "Ecoli.markdup.sorted_CpG.bedGraph:md5,00132adede8128b3a111136713a2a4ff", - "SRR389222.markdup.sorted_CpG.bedGraph:md5,febd0f93f46dfccabf69dbba3f518add", + "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", + "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", + "SRR389222_sub3.markdup.sorted_CpG.bedGraph:md5,a91e6b039e9581a9d2ef6f6057918b39", "Ecoli.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", - "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "SRR389222_sub1.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "SRR389222_sub2.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "SRR389222_sub3.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", "genome_results.txt:md5,d1a1b49086982318f0f94ba7059f71a3", - "genome_results.txt:md5,c786cc367645cee286360707e2624dca" + "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", + "genome_results.txt:md5,2294badeccd2e8870fd6c60d115687b0", + "genome_results.txt:md5,4da1144933d094185d02f7482c120804" ], - "timestamp": "2023-12-20T03:21:55.358959756" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:52:02.181831818" }, "single_end_rrbs": { "content": [ "Ecoli.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", "Ecoli.stats:md5,46eaf2559610c864bc4d27a08a0645b4", - "SRR389222.flagstat:md5,a90f1bdcb30f4d0597ccf69fe0b37b1f", - "SRR389222.stats:md5,b99800367e21a0c7c0d87e5fe29d9609", + "SRR389222_sub1.flagstat:md5,897d500a710a56a7098172167fa71108", + "SRR389222_sub1.stats:md5,0d43bc949dd52241bf6616672bf9409a", + "SRR389222_sub2.flagstat:md5,37d33d68b31d4550620dc17582a3a750", + "SRR389222_sub2.stats:md5,d663612293502df7d0cec6c6d99f79dc", + "SRR389222_sub3.flagstat:md5,e3e925a7b7356e93d14f5e9e102c55b7", + "SRR389222_sub3.stats:md5,22ece6d2ba9c24b0b7f5d8a49b6e4113", [ [ "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", @@ -59,14 +88,23 @@ "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" ] ], - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "Ecoli.sorted_CpG.bedGraph:md5,41f4218573d5e4ff7016ffb42f13a551", - "SRR389222.sorted_CpG.bedGraph:md5,a754358e8b95db30602aa29835a896bd", + "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", + "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", + "SRR389222_sub3.sorted_CpG.bedGraph:md5,70dcc3836dc9721c2de367d1cf05e815", "Ecoli.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", - "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "SRR389222_sub1.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "SRR389222_sub2.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "SRR389222_sub3.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", "genome_results.txt:md5,cd545aa1ee209a1683374bfb5731ab0c", - "genome_results.txt:md5,199902f9d8f10f73bcb0a1ce29ceca5d" + "genome_results.txt:md5,f01c68dd46ca9ec0af3d6ec926763b75", + "genome_results.txt:md5,ef86f3d113782dae1c9bc1660f9f0ae0", + "genome_results.txt:md5,d7700df4fc6f5b66503ea74d02f1b01b" ], - "timestamp": "2023-12-20T03:38:43.324010795" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-21T22:59:17.759034571" } } \ No newline at end of file