From 86581c33df9a009f111382c634233c3b71a8f615 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 26 Aug 2024 17:48:58 +0000 Subject: [PATCH 1/4] produce csi index instead of bai --- conf/modules.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index d7bfbd40..d168ce42 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -314,6 +314,11 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + + withName: 'NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' { + ext.args = '-c' + } + withName: 'NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' { ext.prefix = { "${meta.id}.sorted" } publishDir = [ From d4cc98b673d6657e95bc423b7199174e285fdf12 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 26 Aug 2024 18:24:23 +0000 Subject: [PATCH 2/4] update tests to get csi --- tests/test.nf.test | 48 ++++++++++++++-------------- tests/test_index.nf.test | 32 +++++++++---------- tests/test_mirgenedb.nf.test | 48 ++++++++++++++-------------- tests/test_no_genome.nf.test | 32 +++++++++---------- tests/test_skipfastp.nf.test | 8 ++--- tests/test_technical_repeats.nf.test | 18 +++++------ tests/test_umi.nf.test | 12 +++---- 7 files changed, 99 insertions(+), 99 deletions(-) diff --git a/tests/test.nf.test b/tests/test.nf.test index cbe3a64c..7850ad71 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -69,21 +69,21 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), @@ -109,21 +109,21 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), @@ -233,21 +233,21 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 9800888a..afe190a0 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -52,18 +52,18 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), @@ -95,15 +95,15 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index c9051838..9a7ccdc4 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -74,16 +74,16 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), @@ -113,17 +113,17 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), @@ -194,20 +194,20 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index 2f60b070..77b647df 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -64,22 +64,22 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), @@ -120,22 +120,22 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), diff --git a/tests/test_skipfastp.nf.test b/tests/test_skipfastp.nf.test index 7eae6e2c..1e22c2bc 100644 --- a/tests/test_skipfastp.nf.test +++ b/tests/test_skipfastp.nf.test @@ -36,8 +36,8 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), @@ -46,8 +46,8 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index 9ee71761..43735ef3 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -65,10 +65,10 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), @@ -80,10 +80,10 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), @@ -146,11 +146,11 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index e8d3bdfa..fe605b42 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -86,8 +86,8 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), @@ -104,8 +104,8 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.csi").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.csi").exists(), path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), @@ -160,8 +160,8 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.csi").exists(), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.csi").exists(), path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), From 435f5829ad448a02a2e3af031ccebe1020800b10 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 26 Aug 2024 18:37:02 +0000 Subject: [PATCH 3/4] apply csi to all subworkflows using samtools_index --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index d168ce42..d0200f0c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -315,7 +315,7 @@ process { ] } - withName: 'NFCORE_SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' { + withName: 'SAMTOOLS_INDEX' { ext.args = '-c' } From 7d34115acff2a4cd7f6adb0865ecd9492793b5c3 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Tue, 27 Aug 2024 13:41:05 +0000 Subject: [PATCH 4/4] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 10c6aaed..7a80be59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174) - Add nf-tests for local modules using custom R scripts. - [[#383]](https://github.com/nf-core/smrnaseq/pull/383) - Fix [parameter `--skip_fastp` throws an error](https://github.com/nf-core/smrnaseq/issues/263) - Fix parameter --skip_fastp. - [[#384]](https://github.com/nf-core/smrnaseq/pull/384) - Fix [filter status bug fix](https://github.com/nf-core/smrnaseq/issues/360) - Fix filter stats module and add filter contaminants test profile. +- [[#391]](https://github.com/nf-core/smrnaseq/pull/391) - Change `.bai` index for `.csi` index in `samtools_index` to fix [error because of large chromosomes](https://github.com/nf-core/smrnaseq/issues/132). ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch