Merge remote-tracking branch 'origin/docs' into dev

mskilab-org · Nov 9, 2023 · e4f4d4d · e4f4d4d
2 parents 004910f + 5480070
commit e4f4d4d
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Showing 14 changed files with 518 additions and 181 deletions.
diff --git a/README.md b/README.md
diff --git a/conf/base.config b/conf/base.config
@@ -98,12 +98,12 @@ process {
     }
     withName: 'SVABA' {
         cpus            = { check_max( 16 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 32.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 64.GB * task.attempt, 'memory' ) }
         time            = { check_max( 72.h  * task.attempt, 'time'   ) }
     }
     withName: 'GRIDSS' {
         cpus            = { check_max( 16 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 32.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 64.GB * task.attempt, 'memory' ) }
         time            = { check_max( 72.h  * task.attempt, 'time'    ) }
     }
     withName: 'GRIDSS_SOMATIC' {
@@ -112,25 +112,30 @@ process {
         time            = { check_max( 24.h  * task.attempt, 'time'    ) }
     }
     withName: 'FRAGCOUNTER' {
-        cpus            = { check_max( 10 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 24.GB * task.attempt, 'memory' ) }
+        cpus            = { check_max( 12 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 48.GB * task.attempt, 'memory' ) }
         time            = { check_max( 48.h  * task.attempt, 'time'   ) }
     }
     withName: 'DRYCLEAN' {
-        cpus            = { check_max( 10 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 24.GB * task.attempt, 'memory' ) }
-        time            = { check_max( 24.h  * task.attempt, 'time'    ) }
+        cpus            = { check_max( 8 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 48.GB * task.attempt, 'memory' ) }
+        time            = { check_max( 36.h  * task.attempt, 'time'    ) }
     }
     withName: 'ASCAT_SEG' {
-        cpus            = { check_max( 12 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 24.GB * task.attempt, 'memory' ) }
-        time            = { check_max( 24.h  * task.attempt, 'time'    ) }
+        cpus            = { check_max( 10 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 30.GB * task.attempt, 'memory' ) }
+        time            = { check_max( 10.h  * task.attempt, 'time'    ) }
     }
     withName: 'CBS' {
         cpus            = { check_max( 8 * task.attempt, 'cpus' ) }
-        memory          = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 32.GB * task.attempt, 'memory' ) }
         time            = { check_max( 24.h  * task.attempt, 'time'    ) }
     }
+    withName: 'JABBA' {
+        cpus            = { check_max( 16 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 64.GB * task.attempt, 'memory' ) }
+        time            = { check_max( 12.h  * task.attempt, 'time'    ) }
+    }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }

diff --git a/conf/modules/ascat.config b/conf/modules/ascat.config
@@ -22,7 +22,7 @@ process {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/ASCAT/${meta.id}/" },
-            pattern: "*{rds,png,cnvs.txt,metrics.txt,purityploidy.txt,segments.txt,LogR.txt,BAF.txt}"
+            pattern: "*{rds,png,cnvs.txt,metrics.txt,purityploidy.txt,segments.txt,LogR.txt,BAF.txt,.command.*}"
         ]
     }
 }
diff --git a/conf/modules/cbs.config b/conf/modules/cbs.config
@@ -18,8 +18,8 @@ process {
         ext.when         = { params.tools && params.tools.split(',').contains('cbs') }
         publishDir       = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/cbs/${meta.id}/" },
-                pattern: "*{.rds}"
+                path: { "${params.outdir}/CBS/${meta.id}/" },
+                pattern: "*{.rds,.command.*}"
         ]
     }
 }
diff --git a/conf/modules/dryclean.config b/conf/modules/dryclean.config
@@ -22,7 +22,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/Coverages/Dryclean_tumor/${meta.id}/" },
-                pattern: "*cov.rds"
+                pattern: "*{cov.rds,.command.*}"
         ]
     }
 
@@ -32,7 +32,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/Coverages/Dryclean_normal/${meta.id}/" },
-                pattern: "*cov.rds"
+                pattern: "*{cov.rds,.command.*}"
         ]
     }
 }
diff --git a/conf/modules/fragcounter.config b/conf/modules/fragcounter.config
@@ -21,7 +21,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/Coverages/fragCounter_tumor/${meta.id}/" },
-                pattern: "*{.rds,.bw,cov*}"
+                pattern: "*{.rds,.bw,cov*,.command.*}"
         ]
     }
 
@@ -30,7 +30,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/Coverages/fragCounter_normal/${meta.id}/" },
-                pattern: "*{.rds,.bw,cov*}"
+                pattern: "*{.rds,.bw,cov*,.command.*}"
         ]
     }
 }
diff --git a/conf/modules/hetpileups.config b/conf/modules/hetpileups.config
@@ -19,7 +19,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/Hetpileups/${meta.id}/" },
-                pattern: "*{.txt*}"
+                pattern: "*{.txt*,.command.*}"
         ]
     }
 }
diff --git a/conf/modules/jabba.config b/conf/modules/jabba.config
@@ -18,8 +18,8 @@ process {
         ext.when         = { params.tools && params.tools.split(',').contains('jabba') }
         publishDir       = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/jabba/${meta.id}/" },
-                pattern: "*{.rds,.vcf,.seg}"
+                path: { "${params.outdir}/JaBbA/${meta.id}/" },
+                pattern: "*{.rds*,.vcf,.seg,.png,.txt,.command.*}"
         ]
     }
 }
diff --git a/conf/modules/structural_variants.config b/conf/modules/structural_variants.config
@@ -21,7 +21,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/SV_calling/SVABA/${meta.id}/" },
-                pattern: "*{vcf.gz,txt.gz,vcf*,bam}"
+                pattern: "*{vcf.gz,txt.gz,vcf*,bam,.command.*}"
             ]
     }
 
@@ -31,7 +31,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/SV_calling/GRIDSS/${meta.id}/" },
-                pattern: "*{vcf.gz,txt.gz,vcf*,bam}"
+                pattern: "*{vcf.gz,txt.gz,vcf*,bam,.command.*}"
             ]
     }
 
@@ -40,7 +40,7 @@ process {
         publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/SV_calling/GRIDSS_SOMATIC/${meta.id}/" },
-                pattern: "*{vcf.bgz,vcf.bgz.tbi}"
+                pattern: "*{vcf.bgz,vcf.bgz.tbi,.command.*}"
             ]
     }
 }
diff --git a/docs/README.md b/docs/README.md
@@ -1,10 +1,10 @@
-# nf-core/heisenbio: Documentation
+# mskilab-org/nf-jabba: Documentation
 
-The nf-core/heisenbio documentation is split into the following pages:
+The mskilab-org/nf-jabba documentation is split into the following pages:
 
 - [Usage](usage.md)
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 - [Output](output.md)
   - An overview of the different results produced by the pipeline and how to interpret them.
 
-You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
+You can find a lot more documentation about installing, configuring and running pipelines on the website: [https://nf-co.re](https://nf-co.re)