idk what happened

Author: ljwharbers

conf/modules.config

@@ -42,31 +42,35 @@ process {
     }
 
     withName: '.*:CRAMINO_PRE' {
+        ext.prefix = { "${meta.id}_${meta.type}" }
         ext.args   = '--ubam'
         publishDir = [
             path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_ubam_${meta.replicate}/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.arrow') ? null : filename }
         ]
     }
 
     withName: '.*:CRAMINO_POST' {
+        ext.prefix = { "${meta.id}_${meta.type}" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_aln" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.arrow') ? null : filename }
         ]
     }
 
     withName: '.*:NANOPLOT_PRE' {
+        ext.prefix = { "${meta.id}_${meta.type}_ubam" }
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}/" },
+            path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: '.*:NANOPLOT_POST' {
+        ext.prefix = { "${meta.id}_${meta.type}_aln" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" },
             mode: params.publish_dir_mode,

modules/nf-core/nanoplot/main.nf

@@ -32,6 +32,7 @@ params {
     // Skip options
     skip_qc                     = false
     skip_cramino                = false
+    skip_nanoplot               = false
     skip_mosdepth               = false
     skip_bamstats               = false
     skip_ascat                  = false

nextflow.config

@@ -210,6 +210,10 @@
                 "skip_m6a": {
                     "type": "boolean",
                     "description": "Skip m6a calling by Fibertools"
+                },
+                "skip_nanoplot": {
+                    "type": "boolean",
+                    "description": "Skip Nanoplot"
                 }
             }
         },

nextflow_schema.json

@@ -17,10 +17,11 @@ pipeline_info/*.{html,json,txt,yml}
 */variants/severus/read_ids.csv
 */variants/severus/severus.log
 */variants/severus/{all_SVs,somatic_SVs}/*.{vcf.gz,vcf.gz.tbi}
-*/qc/{tumor,normal}/{cramino_aln}/*_cramino.txt
-*/qc/{tumor,normal}/{cramino_ubam}_*/*_cramino.txt
-*/qc/{tumor,normal}/{nanoplot_ubam}_*/*.html
-*/qc/{tumor,normal}/{nanoplot_aln}/*.html
-*/qc/{tumor,normal}/{nanoplot_ubam}_*/*.txt
-*/qc/{tumor,normal}/{nanoplot_aln}/*.txt
-*/qc/{tumor,normal}/{mosdepth}/*.txt
+*/variants/phased/*.{vcf.gz,vcf.gz.tbi}
+*/qc/{tumor,normal}/cramino_ubam_*/*_cramino.txt
+*/qc/{tumor,normal}/cramino_aln/*_cramino.txt
+*/qc/{tumor,normal}/nanoplot_ubam_*/*.html
+*/qc/{tumor,normal}/nanoplot_aln/*.html
+*/qc/{tumor,normal}/nanoplot_ubam_*/*.txt
+*/qc/{tumor,normal}/nanoplot_aln/*.txt
+*/qc/{tumor,normal}/mosdepth/*.txt