From e707e28a4ad0c55acf1b95a76ff3ad9144e29a0c Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Fri, 26 Jan 2024 14:49:14 +0100
Subject: [PATCH] Final outputpath fixes

---
 conf/modules.config | 44 +++++++++++++++++++++++++++++++++++---------
 1 file changed, 35 insertions(+), 9 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index b6edc20c..b57e4f92 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -73,7 +73,7 @@ process {
             ]
         ]
     }
-    withName: '.*:.*:FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
         ext.args = '--quiet'
         publishDir = [
             path: { "${params.outdir}/fastqc/raw" },
@@ -81,7 +81,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: '.*:.*:FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
         ext.args = '--quiet'
         publishDir = [
             path: { "${params.outdir}/fastqc/trimmed" },
@@ -166,7 +166,7 @@ process {
         ext.args = { meta.single_end ? "--algo ${params.umitools_method} --two-pass" : "--method ${params.umitools_method} --two-pass --paired --remove-unpaired --remove-chimeric" }
         ext.prefix = { "${meta.id}.umi_dedup.sorted" }
         publishDir = [
-            path: { "${params.outdir}/bam_deduplicated" },
+            path: { "${params.outdir}/umi_dedup/bam_deduplicated" },
             mode: params.publish_dir_mode,
             pattern: '*.bam',
             enabled: (
@@ -178,6 +178,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/umi_dedup/fastq_deduplicated" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: (
                 params.save_umi_intermeds
             )
@@ -189,7 +190,8 @@ process {
     //
     withName: 'MIRTRACE_RUN' {
         publishDir = [
-            path: { "${params.outdir}/mirtrace" },
+            //"mirtrace" already part of the published folder
+            path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -237,14 +239,30 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:(BOWTIE_MAP_MATURE|BAM_STATS_MATURE).*' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE' {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/mature" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:(BOWTIE_MAP_HAIRPIN|BAM_STATS_HAIRPIN).*' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:.*' {
+        ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/bam/mature" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/bam/hairpin" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:.*' {
+        ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
             path: { "${params.outdir}/mirna_quant/bam/hairpin" },
             mode: params.publish_dir_mode,
@@ -265,9 +283,17 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/bam/seqcluster" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
     withName: 'MIRTOP_QUANT' {
         publishDir = [
-            path: { "${params.outdir}/mirna_quant/mirtop" },
+            //mirtop already part of the output folder
+            path: { "${params.outdir}/mirna_quant/" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -302,9 +328,9 @@ process {
     }
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME' {
         publishDir = [
-            path: { "${params.outdir}/unmapped/bam" },
+            path: { "${params.outdir}/genome_quant/bam" },
             mode: params.publish_dir_mode,
-            pattern: "unmapped/*.gz"
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }