Get rid of the saveAs in all the modules config of all the modules updated to topic channel

JoseEspinosa · JoseEspinosa · commit 68c4f6d9147a · 2026-03-19T16:44:01.000+01:00
diff --git a/conf/modules.config b/conf/modules.config
@@ -44,7 +44,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
         ]
     }
@@ -54,7 +53,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
         ]
     }
@@ -73,7 +71,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
         ]
     }
@@ -98,7 +95,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
         ]
     }
@@ -170,7 +166,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_align_intermeds
         ]
     }
@@ -179,7 +174,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_align_intermeds
         ]
     }
@@ -189,7 +183,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library/samtools_stats/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_align_intermeds
         ]
     }
@@ -209,7 +202,6 @@ process {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/library" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 enabled: false
             ]
         }
@@ -228,7 +220,6 @@ process {
                 [
                     path: { "${params.outdir}/${params.aligner}/library" },
                     mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                     enabled: false
                 ],
                 [
@@ -500,8 +491,7 @@ process {
             ext.prefix = { "${meta.id}.mLb.mkD" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/preseq" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
@@ -512,26 +502,23 @@ process {
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
         withName: 'DEEPTOOLS_PLOTPROFILE' {
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
         withName: 'DEEPTOOLS_PLOTHEATMAP' {
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
@@ -546,8 +533,7 @@ process {
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotFingerprint" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
@@ -564,8 +550,7 @@ process {
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
@@ -603,8 +588,7 @@ process {
                 ext.args   = '-o ./ -p macs3_peak'
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
 
@@ -613,8 +597,7 @@ process {
                 ext.prefix = 'macs3_annotatePeaks'
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -625,8 +608,7 @@ process {
             ext.prefix = { "${meta.id}.consensus_peaks" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
@@ -635,8 +617,7 @@ process {
             ext.prefix = { "${meta.id}.consensus_peaks" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }

Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,6 @@ process {`
`44`	`44`	`publishDir = [`
`45`	`45`	`path: { "${params.outdir}/genome" },`
`46`	`46`	`mode: params.publish_dir_mode,`
`47`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`48`	`47`	`enabled: params.save_reference`
`49`	`48`	`]`
`50`	`49`	`}`
`@@ -54,7 +53,6 @@ process {`
`54`	`53`	`publishDir = [`
`55`	`54`	`path: { "${params.outdir}/genome/index" },`
`56`	`55`	`mode: params.publish_dir_mode,`
`57`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`58`	`56`	`enabled: params.save_reference`
`59`	`57`	`]`
`60`	`58`	`}`
`@@ -73,7 +71,6 @@ process {`
`73`	`71`	`publishDir = [`
`74`	`72`	`path: { "${params.outdir}/genome" },`
`75`	`73`	`mode: params.publish_dir_mode,`
`76`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`77`	`74`	`enabled: params.save_reference`
`78`	`75`	`]`
`79`	`76`	`}`
`@@ -98,7 +95,6 @@ process {`
`98`	`95`	`publishDir = [`
`99`	`96`	`path: { "${params.outdir}/genome" },`
`100`	`97`	`mode: params.publish_dir_mode,`
`101`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`102`	`98`	`enabled: params.save_reference`
`103`	`99`	`]`
`104`	`100`	`}`
`@@ -170,7 +166,6 @@ process {`
`170`	`166`	`publishDir = [`
`171`	`167`	`path: { "${params.outdir}/${params.aligner}/library" },`
`172`	`168`	`mode: params.publish_dir_mode,`
`173`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`174`	`169`	`enabled: params.save_align_intermeds`
`175`	`170`	`]`
`176`	`171`	`}`
`@@ -179,7 +174,6 @@ process {`
`179`	`174`	`publishDir = [`
`180`	`175`	`path: { "${params.outdir}/${params.aligner}/library" },`
`181`	`176`	`mode: params.publish_dir_mode,`
`182`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`183`	`177`	`enabled: params.save_align_intermeds`
`184`	`178`	`]`
`185`	`179`	`}`
`@@ -189,7 +183,6 @@ process {`
`189`	`183`	`publishDir = [`
`190`	`184`	`path: { "${params.outdir}/${params.aligner}/library/samtools_stats/" },`
`191`	`185`	`mode: params.publish_dir_mode,`
`192`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`193`	`186`	`enabled: params.save_align_intermeds`
`194`	`187`	`]`
`195`	`188`	`}`
`@@ -209,7 +202,6 @@ process {`
`209`	`202`	`publishDir = [`
`210`	`203`	`path: { "${params.outdir}/${params.aligner}/library" },`
`211`	`204`	`mode: params.publish_dir_mode,`
`212`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`213`	`205`	`enabled: false`
`214`	`206`	`]`
`215`	`207`	`}`
`@@ -228,7 +220,6 @@ process {`
`228`	`220`	`[`
`229`	`221`	`path: { "${params.outdir}/${params.aligner}/library" },`
`230`	`222`	`mode: params.publish_dir_mode,`
`231`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`232`	`223`	`enabled: false`
`233`	`224`	`],`
`234`	`225`	`[`
`@@ -500,8 +491,7 @@ process {`
`500`	`491`	`ext.prefix = { "${meta.id}.mLb.mkD" }`
`501`	`492`	`publishDir = [`
`502`	`493`	`path: { "${params.outdir}/${params.aligner}/merged_library/preseq" },`
`503`		`- mode: params.publish_dir_mode,`
`504`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`494`	`+ mode: params.publish_dir_mode`
`505`	`495`	`]`
`506`	`496`	`}`
`507`	`497`	`}`
`@@ -512,26 +502,23 @@ process {`
`512`	`502`	`ext.prefix = { "${meta.id}.mLb.clN" }`
`513`	`503`	`publishDir = [`
`514`	`504`	`path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },`
`515`		`- mode: params.publish_dir_mode,`
`516`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`505`	`+ mode: params.publish_dir_mode`
`517`	`506`	`]`
`518`	`507`	`}`
`519`	`508`
`520`	`509`	`withName: 'DEEPTOOLS_PLOTPROFILE' {`
`521`	`510`	`ext.prefix = { "${meta.id}.mLb.clN" }`
`522`	`511`	`publishDir = [`
`523`	`512`	`path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },`
`524`		`- mode: params.publish_dir_mode,`
`525`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`513`	`+ mode: params.publish_dir_mode`
`526`	`514`	`]`
`527`	`515`	`}`
`528`	`516`
`529`	`517`	`withName: 'DEEPTOOLS_PLOTHEATMAP' {`
`530`	`518`	`ext.prefix = { "${meta.id}.mLb.clN" }`
`531`	`519`	`publishDir = [`
`532`	`520`	`path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },`
`533`		`- mode: params.publish_dir_mode,`
`534`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`521`	`+ mode: params.publish_dir_mode`
`535`	`522`	`]`
`536`	`523`	`}`
`537`	`524`	`}`
`@@ -546,8 +533,7 @@ process {`
`546`	`533`	`ext.prefix = { "${meta.id}.mLb.clN" }`
`547`	`534`	`publishDir = [`
`548`	`535`	`path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotFingerprint" },`
`549`		`- mode: params.publish_dir_mode,`
`550`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`536`	`+ mode: params.publish_dir_mode`
`551`	`537`	`]`
`552`	`538`	`}`
`553`	`539`	`}`
`@@ -564,8 +550,7 @@ process {`
`564`	`550`	`].join(' ').trim()`
`565`	`551`	`publishDir = [`
`566`	`552`	`path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },`
`567`		`- mode: params.publish_dir_mode,`
`568`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`553`	`+ mode: params.publish_dir_mode`
`569`	`554`	`]`
`570`	`555`	`}`
`571`	`556`
`@@ -603,8 +588,7 @@ process {`
`603`	`588`	`ext.args = '-o ./ -p macs3_peak'`
`604`	`589`	`publishDir = [`
`605`	`590`	`path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },`
`606`		`- mode: params.publish_dir_mode,`
`607`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`591`	`+ mode: params.publish_dir_mode`
`608`	`592`	`]`
`609`	`593`	`}`
`610`	`594`
`@@ -613,8 +597,7 @@ process {`
`613`	`597`	`ext.prefix = 'macs3_annotatePeaks'`
`614`	`598`	`publishDir = [`
`615`	`599`	`path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },`
`616`		`- mode: params.publish_dir_mode,`
`617`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`600`	`+ mode: params.publish_dir_mode`
`618`	`601`	`]`
`619`	`602`	`}`
`620`	`603`	`}`
`@@ -625,8 +608,7 @@ process {`
`625`	`608`	`ext.prefix = { "${meta.id}.consensus_peaks" }`
`626`	`609`	`publishDir = [`
`627`	`610`	`path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },`
`628`		`- mode: params.publish_dir_mode,`
`629`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`611`	`+ mode: params.publish_dir_mode`
`630`	`612`	`]`
`631`	`613`	`}`
`632`	`614`
`@@ -635,8 +617,7 @@ process {`
`635`	`617`	`ext.prefix = { "${meta.id}.consensus_peaks" }`
`636`	`618`	`publishDir = [`
`637`	`619`	`path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },`
`638`		`- mode: params.publish_dir_mode,`
`639`		`- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }`
	`620`	`+ mode: params.publish_dir_mode`
`640`	`621`	`]`
`641`	`622`	`}`
`642`	`623`	`}`