From 4d02ff0de813b76af19dcb3cfa66c81980e53303 Mon Sep 17 00:00:00 2001
From: Louis <louislenezet@gmail.com>
Date: Wed, 24 Apr 2024 12:37:49 +0200
Subject: [PATCH] Update result directory configuration

---
 conf/steps/imputation.config          |  2 +-
 conf/steps/imputation_glimpse1.config | 14 +++++---------
 conf/steps/imputation_quilt.config    | 19 +++++++++++--------
 conf/steps/validation.config          | 13 ++++---------
 4 files changed, 21 insertions(+), 27 deletions(-)

diff --git a/conf/steps/imputation.config b/conf/steps/imputation.config
index 93a9776c..7e859eca 100644
--- a/conf/steps/imputation.config
+++ b/conf/steps/imputation.config
@@ -13,7 +13,7 @@
 process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:.*' {
         publishDir = [
-            path: { "${params.outdir}/impute/concat" },
+            path: { "${params.outdir}/imputation/concat" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/conf/steps/imputation_glimpse1.config b/conf/steps/imputation_glimpse1.config
index 30bd848e..5b3d89cd 100644
--- a/conf/steps/imputation_glimpse1.config
+++ b/conf/steps/imputation_glimpse1.config
@@ -56,9 +56,7 @@ process {
             "--buffer-size 20000"
         ].join(' ')
         ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.chunk" }
-        publishDir = [
-            enabled: false
-        ]
+        publishDir = [ enabled: false ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_PHASE' {
@@ -67,19 +65,17 @@ process {
         ].join(' ')
         ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.phase" }
         ext.suffix = "bcf"
-        publishDir = [
-            enabled: false
-        ]
+        publishDir = [ enabled: false ]
     }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:INDEX_PHASE' {
-        publishDir = [
-            enabled: false
-        ]
+        publishDir = [ enabled: false ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_LIGATE' {
         ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.ligate" }
     }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:INDEX_LIGATE' {
         publishDir = [
             path: { "${params.outdir}/imputation/glimpse1" }
diff --git a/conf/steps/imputation_quilt.config b/conf/steps/imputation_quilt.config
index 55069d64..f75c777e 100644
--- a/conf/steps/imputation_quilt.config
+++ b/conf/steps/imputation_quilt.config
@@ -20,7 +20,7 @@ process {
         ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:GLIMPSE_CHUNK' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:.*' {
 
         ext.prefix = { "${meta.id}_${meta.chr}" }
 
@@ -28,12 +28,17 @@ process {
             [
                 path: { "${params.outdir}/imputation/quilt/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}_chunk" },
                 mode: params.publish_dir_mode,
+                enabled: false
             ],
 
 
         ]
     }
 
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:GLIMPSE_CHUNK' {
+        ext.prefix = { "${meta.id}_${meta.chr}" }
+    }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_INDEX' {
         cpus          = 2
         memory        = 400.MB
@@ -76,10 +81,12 @@ process {
         cpus          = 2
         memory        = 400.MB
         maxRetries    = 2
+    }
 
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:.*' {
         publishDir = [
             [
-                path: { "${params.outdir}/quilt_impute/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}/convert" },
+                path: { "${params.outdir}/imputation/quilt/" },
                 mode: params.publish_dir_mode,
             ],
         ]
@@ -87,16 +94,12 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:QUILT_QUILT' {
         ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.impute" }
-        publishDir = [
-            [
-                path: { "${params.outdir}/imputation/quilt/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-                mode: params.publish_dir_mode,
-            ],
-        ]
+        publishDir = [enabled: false]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:INDEX1' {
         ext.args     = "--tbi"
+        publishDir = [enabled: false]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:BCFTOOLS_ANNOTATE' {
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index 14cbf479..e7a8018a 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -17,6 +17,7 @@ process {
             path: { "${params.outdir}/validation/truth" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            enabled: false
         ]
     }
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_MPILEUP' {
@@ -72,9 +73,7 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GLIMPSE2_CONCORDANCE' {
         ext.prefix = { "${meta.id}.concordance" }
         ext.args = "--out-r2-per-site"
-        publishDir = [
-            enabled: false
-        ]
+        publishDir = [ enabled: false ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:CONCATENATE' {
@@ -82,15 +81,11 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GUNZIP' {
-        publishDir = [
-            enabled: false
-        ]
+        publishDir = [ enabled: false ]
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:ADD_COLUMNS' {
         ext.prefix = { "${meta.id}_D${meta.depth}_P${meta.panel}_SNP" }
-        publishDir = [
-            enabled: false
-        ]
+        publishDir = [ enabled: false ]
     }
 }