fixing genrich_sep output dirs

samuelruizperez · Aug 15, 2023 · 7ba93fe · 7ba93fe
1 parent c29d5dd
commit 7ba93fe
Showing 1 changed file with 36 additions and 39 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -721,7 +721,6 @@ if (!params.skip_peak_annotation) {
 }
 
 process {
-
     withName: '.*:MERGED_LIBRARY_NOFILTER_BAM:SAMTOOLS_INDEX' {
         ext.prefix = { "${meta.id}.mLb.sorted" }
         publishDir = [
@@ -799,10 +798,9 @@ process {
 process {
     withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:GENRICH' {
         ext.prefix = { "${meta.id}.mLb" }
-        ext.args   = [
-                        '-j',
-                        params.genrich_pvalue      ? "-p ${params.genrich_pvalue}" : '',
-                        params.genrich_qvalue         ? "-q ${params.genrich_qvalue}" : '',
+        ext.args   = [  '-j',
+                        params.genrich_pvalue            ? "-p ${params.genrich_pvalue}" : '',
+                        params.genrich_qvalue            ? "-q ${params.genrich_qvalue}" : '',
                         params.analyze_multimappers != 0 ? "-s ${params.analyze_multimappers}" : ''
                     ].join(' ').trim()
         publishDir = [
@@ -829,10 +827,22 @@ process {
         ]
     }
 
-    if (!params.skip_peak_annotation) {
+if (!params.skip_peak_annotation) {
+    process {
+        withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:HOMER_ANNOTATEPEAKS' {
+            ext.args   = '-gid'
+            ext.prefix = { "${meta.id}.mLb.genrich.speaks" }
+            publishDir = [
+                path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+    }
+
+    if (params.homer_detail_annotation) {
         process {
-            withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:HOMER_ANNOTATEPEAKS' {
-                ext.args   = '-gid'
+            withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:HOMER_DETAIL_ANNOTATEPEAKS' {
                 ext.prefix = { "${meta.id}.mLb.genrich.speaks" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
@@ -841,40 +851,27 @@ process {
                 ]
             }
         }
+    }
 
-        if (params.homer_detail_annotation) {
-            process {
-                withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:HOMER_DETAIL_ANNOTATEPEAKS' {
-                    ext.prefix = { "${meta.id}.mLb.genrich.speaks" }
-                    publishDir = [
-                        path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
-                        mode: params.publish_dir_mode,
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ]
-                }
+    if (!params.skip_peak_qc) {
+        process {
+            withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_GENRICH_QC' {
+                ext.args   = '-o ./ -p genrich_speak.mLb'
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
             }
-        }
 
-        if (!params.skip_peak_qc) {
-            process {
-                withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_GENRICH_QC' {
-                    ext.args   = '-o ./ -p genrich_speak.mLb'
-                    publishDir = [
-                        path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
-                        mode: params.publish_dir_mode,
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ]
-                }
-
-                withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_HOMER_ANNOTATEPEAKS' {
-                    ext.args   = '-o ./'
-                    ext.prefix = 'genrich_annotate_sPeaks.mLb'
-                    publishDir = [
-                        path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
-                        mode: params.publish_dir_mode,
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ]
-                }
+            withName: '.*:MERGED_LIBRARY_SEP_CALL_ANNOTATE_PEAKS_GENRICH:PLOT_HOMER_ANNOTATEPEAKS' {
+                ext.args   = '-o ./'
+                ext.prefix = 'genrich_annotate_sPeaks.mLb'
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/merged_library/genrich/sep/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
             }
         }
     }