--amend

mskilab-org · May 11, 2024 · 79186bd · 79186bd
1 parent c661907
commit 79186bd
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Showing 4 changed files with 2 additions and 71 deletions.
diff --git a/bin/lp_phased_balance.R b/bin/lp_phased_balance.R
@@ -783,6 +783,7 @@
     }
 
     if(!opt$from_maf) {
+        gg$meta$ploidy = ifelse(is.null(gg$meta$ploidy), NA, gg$meta$ploidy)
         jab = zitools:::gg2jab(gg, purity = gg$meta$purity, ploidy = gg$meta$ploidy)
         jab = jabba.alleles2(jab, hets.gr, verbose = TRUE, uncoupled = TRUE, marginal = opt$marginal)
 

diff --git a/conf/modules/alleic_cn.config b/conf/modules/alleic_cn.config
diff --git a/conf/modules/allelic_cn.config b/conf/modules/allelic_cn.config
@@ -23,24 +23,6 @@ process {
         ]
     }
 
-    withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:NON_INTEGER_BALANCE_WITH_GRIDSS' {
-        ext.when         = { params.tools && params.tools.split(',').contains('alleic_cn') }
-        publishDir       = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/alleic_cn/non_integer_balance_with_gridss/${meta.id}/" },
-                pattern: "*{.rds*,.command.*}"
-        ]
-    }
-
-    withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:NON_INTEGER_BALANCE_WITH_SVABA' {
-        ext.when         = { params.tools && params.tools.split(',').contains('alleic_cn') }
-        publishDir       = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/alleic_cn/non_integer_balance_with_svaba/${meta.id}/" },
-                pattern: "*{.rds*,.command.*}"
-        ]
-    }
-
     withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:LP_PHASED_BALANCE' {
         ext.when         = { params.tools && params.tools.split(',').contains('alleic_cn') }
         publishDir       = [
@@ -49,22 +31,4 @@ process {
                 pattern: "*{.rds*,.command.*}"
         ]
     }
-
-    withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:LP_PHASED_BALANCE_WITH_GRIDSS' {
-        ext.when         = { params.tools && params.tools.split(',').contains('alleic_cn') }
-        publishDir       = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/alleic_cn/lp_phased_balance_with_gridss/${meta.id}/" },
-                pattern: "*{.rds*,.command.*}"
-        ]
-    }
-
-    withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:LP_PHASED_BALANCE_WITH_SVABA' {
-        ext.when         = { params.tools && params.tools.split(',').contains('alleic_cn') }
-        publishDir       = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/alleic_cn/lp_phased_balance_with_svaba/${meta.id}/" },
-                pattern: "*{.rds*,.command.*}"
-        ]
-    }
 }
diff --git a/conf/modules/events.config b/conf/modules/events.config
@@ -18,7 +18,7 @@ process {
         ext.when         = { params.tools && params.tools.split(',').contains('events') }
         publishDir       = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/events/${meta.id}/" },
+                path: { "${params.outdir}/Events/${meta.id}/" },
                 pattern: "*{.rds*,.command.*}"
         ]
     }