From bfa627289af818e8737abfc6b56c5ed7269bbcd4 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Apr 2023 20:34:32 +0200
Subject: [PATCH 1/2] CHORES: update ALL bcftools modules

---
 modules/nf-core/bcftools/call/main.nf      | 6 +++---
 modules/nf-core/bcftools/concat/main.nf    | 6 +++---
 modules/nf-core/bcftools/consensus/main.nf | 6 +++---
 modules/nf-core/bcftools/convert/main.nf   | 6 +++---
 modules/nf-core/bcftools/filter/main.nf    | 6 +++---
 modules/nf-core/bcftools/index/main.nf     | 6 +++---
 modules/nf-core/bcftools/isec/main.nf      | 6 +++---
 modules/nf-core/bcftools/merge/main.nf     | 6 +++---
 modules/nf-core/bcftools/mpileup/main.nf   | 6 +++---
 modules/nf-core/bcftools/norm/main.nf      | 6 +++---
 modules/nf-core/bcftools/query/main.nf     | 6 +++---
 modules/nf-core/bcftools/reheader/main.nf  | 6 +++---
 modules/nf-core/bcftools/roh/main.nf       | 6 +++---
 modules/nf-core/bcftools/sort/main.nf      | 6 +++---
 modules/nf-core/bcftools/split/main.nf     | 6 +++---
 modules/nf-core/bcftools/stats/main.nf     | 6 +++---
 modules/nf-core/bcftools/view/main.nf      | 6 +++---
 17 files changed, 51 insertions(+), 51 deletions(-)

diff --git a/modules/nf-core/bcftools/call/main.nf b/modules/nf-core/bcftools/call/main.nf
index 3506b824f3a..ebb69088c15 100644
--- a/modules/nf-core/bcftools/call/main.nf
+++ b/modules/nf-core/bcftools/call/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_CALL {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
index c7c39d9fa0d..de9ba6727cd 100644
--- a/modules/nf-core/bcftools/concat/main.nf
+++ b/modules/nf-core/bcftools/concat/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbi)
diff --git a/modules/nf-core/bcftools/consensus/main.nf b/modules/nf-core/bcftools/consensus/main.nf
index a32d94b17c9..db2c758a58d 100644
--- a/modules/nf-core/bcftools/consensus/main.nf
+++ b/modules/nf-core/bcftools/consensus/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(fasta)
diff --git a/modules/nf-core/bcftools/convert/main.nf b/modules/nf-core/bcftools/convert/main.nf
index d748c75fbb5..fea4df1911b 100644
--- a/modules/nf-core/bcftools/convert/main.nf
+++ b/modules/nf-core/bcftools/convert/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_CONVERT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
index 4e02009d292..4ee7684cb56 100644
--- a/modules/nf-core/bcftools/filter/main.nf
+++ b/modules/nf-core/bcftools/filter/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
index f1c897cde68..c99b981c1f9 100644
--- a/modules/nf-core/bcftools/index/main.nf
+++ b/modules/nf-core/bcftools/index/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/bcftools/isec/main.nf b/modules/nf-core/bcftools/isec/main.nf
index 67a19e71ccb..95234d654d6 100644
--- a/modules/nf-core/bcftools/isec/main.nf
+++ b/modules/nf-core/bcftools/isec/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
index e664f0eb843..972b2a747b3 100644
--- a/modules/nf-core/bcftools/merge/main.nf
+++ b/modules/nf-core/bcftools/merge/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
index c9e42c4dd5a..319ce883122 100644
--- a/modules/nf-core/bcftools/mpileup/main.nf
+++ b/modules/nf-core/bcftools/mpileup/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(bam), path(intervals)
diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf
index 90387d6cef0..efd5bb91da5 100644
--- a/modules/nf-core/bcftools/norm/main.nf
+++ b/modules/nf-core/bcftools/norm/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
index 5a917b3e86b..8e1c10b1657 100644
--- a/modules/nf-core/bcftools/query/main.nf
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf
index 57634c073a6..d817af23132 100644
--- a/modules/nf-core/bcftools/reheader/main.nf
+++ b/modules/nf-core/bcftools/reheader/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(header)
diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf
index dc516b029de..4624341199c 100644
--- a/modules/nf-core/bcftools/roh/main.nf
+++ b/modules/nf-core/bcftools/roh/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_ROH {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
index 9ae3253b69e..69d933412e4 100644
--- a/modules/nf-core/bcftools/sort/main.nf
+++ b/modules/nf-core/bcftools/sort/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/bcftools/split/main.nf b/modules/nf-core/bcftools/split/main.nf
index 42bfc23f453..ccb3e2f248e 100644
--- a/modules/nf-core/bcftools/split/main.nf
+++ b/modules/nf-core/bcftools/split/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
index 51e9c91c708..49685f0aa83 100644
--- a/modules/nf-core/bcftools/stats/main.nf
+++ b/modules/nf-core/bcftools/stats/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
index 04ced9c9adb..01a58823f27 100644
--- a/modules/nf-core/bcftools/view/main.nf
+++ b/modules/nf-core/bcftools/view/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bcftools=1.16"
+    conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
-        'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
+        'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)

From 17530387d9cf03d7bede633d228760cce4f1e85c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Wed, 26 Apr 2023 20:47:40 +0200
Subject: [PATCH 2/2] update md5sum

---
 .../modules/nf-core/bcftools/mpileup/test.yml | 20 +++++++++----------
 .../test.yml                                  |  1 -
 2 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/tests/modules/nf-core/bcftools/mpileup/test.yml b/tests/modules/nf-core/bcftools/mpileup/test.yml
index 05eedc25887..0ee9121fc69 100644
--- a/tests/modules/nf-core/bcftools/mpileup/test.yml
+++ b/tests/modules/nf-core/bcftools/mpileup/test.yml
@@ -5,11 +5,11 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 0a6fb5b79930bb2c3c179619380e8ebf
+      md5sum: 652ead9184c18167613a3bfc75b99111
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 2198b362ec46027623f2cc5da5881777
+      md5sum: 23e5a910227891c53bb34196be7c00b4
     - path: output/bcftools/test.vcf.gz
-      md5sum: f0e3b1b665205909b52226473b5bf8fb
+      md5sum: 960b84036dd0a532b338b1a95813fc25
 
 - name: bcftools mpileup test_bcftools_save_mpileup
   command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config
@@ -18,13 +18,13 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 0a6fb5b79930bb2c3c179619380e8ebf
+      md5sum: 652ead9184c18167613a3bfc75b99111
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 2198b362ec46027623f2cc5da5881777
+      md5sum: 23e5a910227891c53bb34196be7c00b4
     - path: output/bcftools/test.vcf.gz
-      md5sum: f0e3b1b665205909b52226473b5bf8fb
+      md5sum: 960b84036dd0a532b338b1a95813fc25
     - path: output/bcftools/test.mpileup.gz
-      md5sum: 175e7e6edf0ca24bf6cfffe5a3bf7061
+      md5sum: dd424be36720bb09007233bd367796f1
 
 - name: bcftools mpileup test_bcftools_mpileup_intervals
   command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_mpileup_intervals -c ./tests/config/nextflow.config     -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config
@@ -33,8 +33,8 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: d91d947ec3822ecabf28d474babc303c
+      md5sum: 405eee1f452446e34f3dcfc2b00e5fab
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: d655c592ab8ef5c834cdd19dc1022fec
+      md5sum: 3a50baca0fb70eaab68c44cb9bd4d4a3
     - path: output/bcftools/test.vcf.gz
-      md5sum: d0e1b95b45610fe37bee5712a9bb0124
+      md5sum: 1feaf4810f6b57f32ea7fd2dbc4da9a0
diff --git a/tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/test.yml b/tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/test.yml
index 97227984095..3a9df7ca582 100644
--- a/tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/test.yml
+++ b/tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/test.yml
@@ -12,7 +12,6 @@
       contains:
         - "chr22\t1982\t.\tA\tG\t459.724"
     - path: output/bcftools/aligned.sorted.vcf.gz.csi
-      md5sum: 93ecb3ee8fb165cbd754e1a1676e41fe
     - path: output/freebayes/aligned.vcf.gz
       contains:
         - "chr22\t1982\t.\tA\tG\t459.724"