better log file fix

Author: pinin4fjords

conf/test.config

@@ -41,6 +41,10 @@ params {
     skip_bbsplit        = false
     pseudo_aligner      = 'salmon'
     umitools_bc_pattern = 'NNNN'
+
+    remove_ribo_rna= true
+    sortmerna_index = '/Users/jonathan.manning/projects/rnaseq/idx'
+    skip_multiqc = true
 }
 
 // When using RSEM, remove warning from STAR whilst building tiny indices

workflows/rnaseq/nextflow.config

@@ -137,11 +137,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMI(COLLAPSE|TOOLS)_TRANSCRIPTOME:UMI(COLLAPSE|TOOLS_DEDUP)' {
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
                 publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.{log,tsv}'
-                    ],
                     [
                         path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                         mode: params.publish_dir_mode,
@@ -240,20 +235,60 @@ if (!params.skip_alignment) {
                 ext.prefix = { "${meta.id}.umi_dedup.sorted" }
                 publishDir = [
                     [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
+                        path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
                         mode: params.publish_dir_mode,
-                        pattern: '*.tsv'
-                    ],
+                        pattern: '*.bam',
+                        saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umicollapse/genomic_dedup_log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME:UMICOLLAPSE' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umicollapse/transcriptomic_dedup_log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS' {
+                publishDir = [
                     [
                         path: { "${params.outdir}/${params.aligner}/umitools/genomic_dedup_log" },
                         mode: params.publish_dir_mode,
                         pattern: '*.log'
+                    ]
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS' {
+                publishDir = [
+                    [
+                        path: { "${params.outdir}/${params.aligner}/umitools/transcriptomic_dedup_log" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log'
                     ],
+                ]
+            }
+
+            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_(GEN_TRANSCRIP)TOME:UMITOOLS' {
+                publishDir = [
                     [
-                        path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
+                        path: { "${params.outdir}/${params.aligner}/umitools" },
                         mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
+                        pattern: '*.tsv'
                     ]
                 ]
             }