Merge pull request #402 from bjlang/dev

Clean up and removal of double slashes
nf-core · Jul 11, 2024 · 637deb5 · 637deb5
2 parents a1dd9c2 + 1bd1b15
commit 637deb5
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Showing 4 changed files with 18 additions and 26 deletions.
diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@
 
 ## Introduction
 
-**nfcore/chipseq** is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data.
+**nfcore/chipseq** is a bioinformatics analysis pipeline used for Chromatin ImmunoPrecipitation sequencing (ChIP-seq) data.
 
 On release, automated continuous integration tests run the pipeline on a [full-sized dataset](https://github.com/nf-core/test-datasets/tree/chipseq#full-test-dataset-origin) on the AWS cloud infrastructure. The dataset consists of FoxA1 (transcription factor) and EZH2 (histone,mark) IP experiments from _Franco et al. 2015_ ([GEO: GSE59530](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59530), [PMID: 25752574](https://pubmed.ncbi.nlm.nih.gov/25752574/)) and _Popovic et al. 2014_ ([GEO: GSE57632](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57632), [PMID: 25188243](https://pubmed.ncbi.nlm.nih.gov/25188243/)), respectively. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from running the full-sized tests can be viewed on the [nf-core website](https://nf-co.re/chipseq/results).
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -550,10 +550,7 @@ process {
             params.aligner == "chromap" ? "--format BAM" : '' //TODO check if not needed anymore with new chromap versions
         ].join(' ').trim()
         publishDir = [
-            path: { [
-                "${params.outdir}/${params.aligner}/merged_library/macs2",
-                params.narrow_peak? '/narrow_peak' : '/broad_peak'
-            ].join('') },
+            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -562,14 +559,14 @@ process {
     withName: 'FRIP_SCORE' {
         ext.args   = '-bed -c -f 0.20'
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
             enabled: false
         ]
     }
 
     withName: 'MULTIQC_CUSTOM_PEAKS' {
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -582,7 +579,7 @@ if (!params.skip_peak_annotation) {
             ext.args   = '-gid'
             ext.prefix = { "${meta.id}_peaks" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -594,7 +591,7 @@ if (!params.skip_peak_annotation) {
             withName: 'PLOT_MACS2_QC' {
                 ext.args   = '-o ./ -p macs2_peak'
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -604,7 +601,7 @@ if (!params.skip_peak_annotation) {
                 ext.args   = '-o ./'
                 ext.prefix = 'macs2_annotatePeaks'
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -619,7 +616,7 @@ if (!params.skip_consensus_peaks) {
             ext.when   = { meta.multiple_groups || meta.replicates_exist }
             ext.prefix = { "${meta.id}.consensus_peaks" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -629,7 +626,7 @@ if (!params.skip_consensus_peaks) {
             ext.args   = '-F SAF -O --fracOverlap 0.2'
             ext.prefix = { "${meta.id}.consensus_peaks" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -642,7 +639,7 @@ if (!params.skip_consensus_peaks) {
                 ext.args   = '-gid'
                 ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -651,7 +648,7 @@ if (!params.skip_consensus_peaks) {
             withName: 'ANNOTATE_BOOLEAN_PEAKS' {
                 ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -671,7 +668,7 @@ if (!params.skip_consensus_peaks) {
                 ].join(' ').trim()
                 ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}/deseq2" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}/deseq2" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -685,7 +682,7 @@ if (!params.skip_igv) {
         withName: 'IGV' {
             publishDir = [
                 [
-                        path: { "${params.outdir}/igv/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
+                        path: { "${params.outdir}/igv/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
                         mode: params.publish_dir_mode,
                         pattern: '*.{txt,xml}'
                 ],
@@ -704,7 +701,7 @@ if (!params.skip_multiqc) {
         withName: 'MULTIQC' {
             ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
             publishDir = [
-                path: { "${params.outdir}/multiqc/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
+                path: { "${params.outdir}/multiqc/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]

diff --git a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf b/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf
@@ -30,7 +30,7 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
     ch_peaks
         .map {
             meta, peak ->
-                [ meta.antibody, meta.id.split('_')[0..-2].join('_'), peak ]
+                [ meta.antibody, meta.id - ~/_T\d+$/, peak ]
         }
         .groupTuple()
         .map {

diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
@@ -7,8 +7,6 @@
 //
 // MODULE: Loaded from modules/local/
 //
-include { MACS2_CONSENSUS                     } from '../modules/local/macs2_consensus'
-include { DESEQ2_QC                           } from '../modules/local/deseq2_qc'
 include { IGV                                 } from '../modules/local/igv'
 include { MULTIQC                             } from '../modules/local/multiqc'
 include { MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS } from '../modules/local/multiqc_custom_phantompeakqualtools'
@@ -46,9 +44,6 @@ include { DEEPTOOLS_PLOTPROFILE         } from '../modules/nf-core/deeptools/plo
 include { DEEPTOOLS_PLOTHEATMAP         } from '../modules/nf-core/deeptools/plotheatmap/main'
 include { DEEPTOOLS_PLOTFINGERPRINT     } from '../modules/nf-core/deeptools/plotfingerprint/main'
 include { KHMER_UNIQUEKMERS             } from '../modules/nf-core/khmer/uniquekmers/main'
-include { SUBREAD_FEATURECOUNTS         } from '../modules/nf-core/subread/featurecounts/main'
-
-include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_CONSENSUS } from '../modules/nf-core/homer/annotatepeaks/main'
 
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
@@ -240,13 +235,13 @@ workflow CHIPSEQ {
             meta, bam ->
                 def meta_clone = meta.clone()
                 meta_clone.remove('read_group')
-                meta_clone.id = meta_clone.id.split('_')[0..-2].join('_')
+                meta_clone.id = meta_clone.id - ~/_T\d+$/
                 [ meta_clone, bam ]
         }
         .groupTuple(by: [0])
         .map {
-            it ->
-                [ it[0], it[1].flatten() ]
+            meta, bam ->
+                [ meta, bam.flatten() ]
         }
         .set { ch_sort_bam }