update modules.config

nf-core · Sep 25, 2023 · 889df95 · 889df95
1 parent 992636f
commit 889df95
Showing 1 changed file with 3 additions and 70 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -133,14 +133,6 @@ process {
         ]
     }
 
-    withName: KALLISTO_INDEX {
-        ext.args = '-k 31'
-        publishDir = [
-            path: { "${params.genomes_base}/pizzly" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
     withName: MEGAFUSION {
         ext.when = {!params.fusioninspector_only}
         ext.prefix = { "${meta.id}_fusion_data" }
@@ -157,20 +149,16 @@ process {
 
     }
 
-    withName: PICARD_MARKDUPLICATES {
+    withName: GATK4_MARKDUPLICATES {
         ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) }
-    }
-
-    withName: PIZZLY {
-        ext.args = "-k 31 --align-score 2 --insert-size 400 --cache index.cache.txt"
         publishDir = [
-            path: { "${params.outdir}/pizzly" },
+            path: { "${params.outdir}/picard" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: QUALIMAP_RNASEQ {
+    withName: MOSDEPTH {
         ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)}
     }
 
@@ -203,15 +191,6 @@ process {
         ]
     }
 
-    withName: SAMTOOLS_SORT_FOR_SQUID_CHIMERIC {
-        ext.prefix = { "${meta.id}_chimeric_sorted" }
-        publishDir = [
-            path: { "${params.outdir}/samtools_sort_for_squid_chimeric" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: SAMTOOLS_VIEW_FOR_ARRIBA {
         ext.args = { "--output-fmt cram" }
         ext.prefix = { "${meta.id}_star_for_arriba" }
@@ -222,35 +201,6 @@ process {
         ]
     }
 
-    withName: SAMTOOLS_VIEW_FOR_SQUID_CHIMERIC {
-        ext.prefix = { "${meta.id}_chimeric" }
-        ext.args = { "--output-fmt bam" }
-        publishDir = [
-            path: { "${params.outdir}/samtools_view_for_squid_chimeric" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM {
-        ext.args = { "--output-fmt cram" }
-        publishDir = [
-            path: { "${params.outdir}/cram_squid" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM_CHIMERIC {
-        ext.args = { "--output-fmt cram" }
-        ext.prefix = { "${meta.id}_chimeric" }
-        publishDir = [
-            path: { "${params.outdir}/cram_squid" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: SAMTOOLS_VIEW_FOR_STARFUSION {
         ext.args = { "--output-fmt cram" }
         ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" }
@@ -285,23 +235,6 @@ process {
         --chimMultimapNmax 50'
     }
 
-    withName: STAR_FOR_SQUID {
-        publishDir = [
-            path: { "${params.outdir}/star_for_squid" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-        ext.args = '--twopassMode Basic \
-        --chimOutType SeparateSAMold \
-        --chimSegmentMin 20 \
-        --chimJunctionOverhangMin 12 \
-        --alignSJDBoverhangMin 10 \
-        --outReadsUnmapped Fastx \
-        --outSAMstrandField intronMotif \
-        --outSAMtype BAM SortedByCoordinate \
-        --readFilesCommand zcat'
-    }
-
     withName: STAR_FOR_STARFUSION {
         publishDir = [
             path: { "${params.outdir}/star_for_starfusion" },