Adding code to split bam on chromosome in order to try and paralleliz…

…e and speed up umitools dedup. Also tweaking some of structure of the results folder

conf/modules.config

@@ -169,14 +169,38 @@ if (!params.skip_qc){
 
     process {
         withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:BAM_STATS_SAMTOOLS:.*' {
-            ext.prefix = { "${meta.id}.dedup" }
+            ext.prefix = { "${meta.id}.dedup.sorted" }
             publishDir = [
-                path: { "${params.outdir}/${meta.id}/qc/samtools/dedup" },
+                path: { "${params.outdir}/${meta.id}/bam/dedup" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
     }
+
+    process {
+        withName:'.*:BAM_SORT_STATS_SAMTOOLS_SPLIT:BAM_STATS_SAMTOOLS:.*' {
+            ext.prefix = { "${meta.id}.sorted" }
+            publishDir = [
+                enabled: false
+            ]
+        }
+    }
+}
+
+if (!params.skip_qc) {
+
+    process {
+        withName:'.*:RSEQC_READDISTRIBUTION' {
+            publishDir = [
+                path: { "${params.outdir}/${meta.id}/qc/rseqc" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+    }
+
 }
 
 /////////////////////
@@ -224,6 +248,23 @@ if (!params.skip_save_minimap2_index) {
     }
 }
 
+process {
+    withName: '.*:UCSC_GTFTOGENEPRED' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
+
+process {
+    withName: '.*:UCSC_GENEPREDTOBED' {
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
+
+
 //////////////////////
 // FASTQ PROCESSING //
 //////////////////////
@@ -394,6 +435,7 @@ process {
 
 process {
     withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:SAMTOOLS_SORT' {
+        ext.prefix = { "${meta.id}.dedup.sorted" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/bam/dedup" },
             mode: params.publish_dir_mode,
@@ -402,6 +444,15 @@ process {
     }
 }
 
+process {
+    withName:'.*:BAM_SORT_STATS_SAMTOOLS_SPLIT:.*' {
+        ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
+
 // SAMTOOLS_INDEX
 
 process {
@@ -436,6 +487,7 @@ process {
 
 process {
     withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:SAMTOOLS_INDEX' {
+        ext.prefix = { "${meta.id}.dedup.sorted" }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/bam/dedup" },
             mode: params.publish_dir_mode,
@@ -444,6 +496,14 @@ process {
     }
 }
 
+process {
+    withName:'.*:SAMTOOLS_MERGE'{
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
+
 ////////////////////////
 // BARCODE CORRECTION //
 ////////////////////////
@@ -472,13 +532,24 @@ process {
 // UMI DEDUPLICATION //
 ///////////////////////
 
+process {
+    withName: '.*:BAMTOOLS_SPLIT' {
+        ext.args = {
+            [
+                "-reference"
+            ].join(' ').trim()
+        }
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
+
 process {
     withName: '.*:UMITOOLS_DEDUP' {
         ext.prefix = { "${meta.id}.dedup" }
         publishDir = [
-            path: { "${params.outdir}/${meta.id}/bam/dedup" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            enabled: false
         ]
     }
 }

modules.json

@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bamtools/split": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -65,6 +70,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
+                    "samtools/merge": {
+                        "branch": "master",
+                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",