From 53ef005f0a1387c320ce6b3cf25363794fe7dde9 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Nov 2024 15:35:52 +0100
Subject: [PATCH 1/4] put fastp results in own directory

---
 conf/modules.config | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 09fbff1fc..aace67cf4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -103,13 +103,13 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         publishDir = [
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/fastp" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.preprocessing_savepreprocessedreads
             ],
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/fastp" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{log,html,json}'
             ]
@@ -133,13 +133,13 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         publishDir = [
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/fastp" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.preprocessing_savepreprocessedreads
             ],
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/fastp" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{log,html,json}'
             ]

From d36dee2660a7c96059642e80e62232aa722ccf90 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Nov 2024 15:36:45 +0100
Subject: [PATCH 2/4] Put adapter removal results in own directory

---
 conf/modules.config | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index aace67cf4..612e83d46 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -165,13 +165,13 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         publishDir = [
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.preprocessing_savepreprocessedreads
             ],
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.settings'
             ]
@@ -199,13 +199,13 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
         publishDir = [
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.preprocessing_savepreprocessedreads
             ],
             [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.settings'
             ]
@@ -216,7 +216,7 @@ process {
         tag = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
         publishDir = [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/preprocessing/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.preprocessing_savepreprocessedreads

From 038ab3d3028514704fe54c391a16ac404fdaba75 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Nov 2024 15:37:49 +0100
Subject: [PATCH 3/4] fix bam_filtering result directory name. Minor formatting
 changes

---
 conf/modules.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 612e83d46..7608564d9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -335,7 +335,7 @@ process {
         tag = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
         publishDir = [
-                path: { "${params.outdir}/preprocessing" },
+                path: { "${params.outdir}/bam_filtering/" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.preprocessing_savepreprocessedreads
@@ -862,7 +862,7 @@ process {
             path: { "${params.outdir}/damage_manipulation/" },
             mode: params.publish_dir_mode,
             pattern: '*.{bai,csi}'
-            ]
+        ]
     }
 
     //
@@ -1115,7 +1115,7 @@ process {
         ext.prefix = { "${meta2.id}_samtoolsdepth" }
         ext.args = '-aa -q30 -Q30 -H'
         publishDir = [
-        enabled: false
+            enabled: false
         ]
     }
 

From 9ae841589cd3d7624282495d7a25e6880dcb9313 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Nov 2024 15:38:38 +0100
Subject: [PATCH 4/4] exclude versions.yml from published results. remove
 enabled:true statements from publishDirs.

---
 conf/modules.config | 51 ++++++++++++++++++++++-----------------------
 1 file changed, 25 insertions(+), 26 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 7608564d9..67e030eef 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -47,6 +47,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/fastqc_raw/" },
             mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -57,6 +58,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/fastqc_processed/" },
             mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -76,6 +78,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/falco_raw/" },
             mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -86,6 +89,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/falco_processed/" },
             mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -704,7 +708,8 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
         publishDir = [
             path: { "${params.outdir}/mapstats/preseq" },
-            mode: params.publish_dir_mode
+            mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -722,7 +727,8 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}" }
         publishDir = [
             path: { "${params.outdir}/mapstats/preseq" },
-            mode: params.publish_dir_mode
+            mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -742,7 +748,8 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.reference}_depth" }
         publishDir = [
             path: { "${params.outdir}/mapstats/bedtools" },
-            mode: params.publish_dir_mode
+            mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -752,7 +759,8 @@ process {
         ext.prefix = { "${meta.sample_id}_${meta.reference}_breadth" }
         publishDir = [
             path: { "${params.outdir}/mapstats/bedtools" },
-            mode: params.publish_dir_mode
+            mode: params.publish_dir_mode,
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -1066,9 +1074,9 @@ process {
     withName: 'QUALIMAP_BAMQC_WITHBED|QUALIMAP_BAMQC_NOBED' {
         tag = { "${meta.reference}|${meta.sample_id}" }
         publishDir = [
-            path: { "${params.outdir}/mapstats/qualimap/${meta.reference}/${meta.sample_id}/}" },
+            path: { "${params.outdir}/mapstats/qualimap/${meta.reference}/" },
             mode: params.publish_dir_mode,
-            enabled: true
+            pattern: '*[!versions.yml]',
         ]
     }
 
@@ -1086,7 +1094,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/damage_estimation/damageprofiler/" },
             mode: params.publish_dir_mode,
-            enabled: true
+            pattern: '*[!versions.yml]'
         ]
     }
 
@@ -1250,8 +1258,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.{geno,snp,ind}'
+            pattern: '*.{geno,snp,ind}',
         ]
     }
 
@@ -1262,8 +1269,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.{tsv}'
+            pattern: '*.{tsv}',
         ]
     }
 
@@ -1285,9 +1291,9 @@ process {
         ].join(' ').trim()
         ext.prefix = { "${meta.sample_id}_${meta.reference}_realigned" }
         publishDir = [
+            enabled: params.genotyping_gatk_ug_keeprealignbam,
             path: { "${params.outdir}/genotyping/IndelRealigner" },
             mode: params.publish_dir_mode,
-            enabled: params.genotyping_gatk_ug_keeprealignbam,
             pattern: '*.{bam,bai}'
         ]
     }
@@ -1306,8 +1312,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.vcf.gz'
+            pattern: '*.vcf.gz',
         ]
     }
 
@@ -1318,8 +1323,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.vcf.gz.tbi'
+            pattern: '*.vcf.gz.tbi',
         ]
     }
 
@@ -1336,8 +1340,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.{vcf.gz,vcf.gz.tbi}'
+            pattern: '*.{vcf.gz,vcf.gz.tbi}',
         ]
     }
 
@@ -1352,8 +1355,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.vcf.gz'
+            pattern: '*.vcf.gz',
         ]
     }
 
@@ -1364,8 +1366,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.vcf.gz.tbi'
+            pattern: '*.vcf.gz.tbi',
         ]
     }
 
@@ -1375,8 +1376,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.txt'
+            pattern: '*.txt',
         ]
     }
 
@@ -1395,8 +1395,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genotyping/" },
             mode: params.publish_dir_mode,
-            enabled: true,
-            pattern: '*.{glf,beagle}.gz'
+            pattern: '*.{glf,beagle}.gz',
         ]
     }
 }