update samtools version to 1.15 (#1358)

* update samtools version to 1.15

* Update checksums

modules/samtools/ampliconclip/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_AMPLICONCLIP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/bam2fq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(inputbam)

modules/samtools/depth/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_DEPTH {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/faidx/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(fasta)

modules/samtools/fastq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/fixmate/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FIXMATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/flagstat/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/samtools/idxstats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/samtools/index/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input)

modules/samtools/merge/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_MERGE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input_files)

modules/samtools/mpileup/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/sort/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/stats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input), path(input_index)

modules/samtools/view/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input)

tests/modules/samtools/ampliconclip/test.yml

@@ -5,7 +5,7 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 678f9ab04fbe3206f0f96e170fd833e9
+      md5sum: 5d0e8bc9e6059ef3a63ee6328a3935c7
 
 - name: samtools ampliconclip no stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -14,9 +14,9 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: bbf65ea626539d96c8271e17d1fc988b
+      md5sum: 2c998295d624c59620b7ffdb0cc080e2
     - path: output/samtools/test.cliprejects.bam
-      md5sum: a0bee15aead020d16d0c81bd9667df46
+      md5sum: f3ebba8d91ad29cc4d2d00943e6f6bab
 
 - name: samtools ampliconclip with stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -25,8 +25,8 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: f5a3611ecad34ba2dde77096e1c7dd93
+      md5sum: 87882973b425ab27aad6ef18faf11f25
     - path: output/samtools/test.cliprejects.bam
-      md5sum: 90ee7ce908b4bdb89ab41e4410de9012
+      md5sum: eb5e186e1a69864dc2e99a290f02ff78
     - path: output/samtools/test.clipstats.txt
       md5sum: fc23355e1743d47f2541f2cb1a7a0cda

tests/modules/samtools/bam2fq/test.yml

@@ -14,9 +14,9 @@
     - samtools
   files:
     - path: output/samtools/test_1.fq.gz
-      md5sum: 4522edbe158ec4804765794569f67493
+      md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed
     - path: output/samtools/test_2.fq.gz
-      md5sum: 7e00ef40d5cfe272b67461381019dcc1
+      md5sum: e679ec035d3208785e704458d6b68c8c
     - path: output/samtools/test_other.fq.gz
       md5sum: 709872fc2910431b1e8b7074bfe38c67
     - path: output/samtools/test_singleton.fq.gz

tests/modules/samtools/faidx/test.yml

@@ -7,4 +7,4 @@
     - path: output/samtools/genome.fasta.fai
       md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
     - path: output/samtools/versions.yml
-      md5sum: d56671a7c8f8058944d3d536c3058f7f
+      md5sum: 6a16b2148a0ab43e6d0506056e6a0409

tests/modules/samtools/fastq/test.yml

@@ -5,6 +5,6 @@
     - samtools/fastq
   files:
     - path: output/samtools/test_2.fastq.gz
-      md5sum: 3b1c92f33a44a78d82f8360ab4fdfd61
+      md5sum: 51e7a469b554de694799bec982fd722e
     - path: output/samtools/test_1.fastq.gz
-      md5sum: 5a3f9c69a032c4ffd9071ea31a14e6f9
+      md5sum: 6c2d5b467eb94e058300271a542e34e6

tests/modules/samtools/fixmate/test.yml

@@ -5,4 +5,4 @@
     - samtools/fixmate
   files:
     - path: output/samtools/test.bam
-      md5sum: a4092657a4b17170c7702a76cbf192a1
+      md5sum: c7f574bb0c469e0ccfecb6b7210e03c5

tests/modules/samtools/index/test.yml

@@ -23,4 +23,4 @@
     - samtools/index
   files:
     - path: output/samtools/test.paired_end.sorted.bam.csi
-      md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd
+      md5sum: 8d63373007553e74d823fc2b9cbcf84d

tests/modules/samtools/sort/test.yml

@@ -5,4 +5,4 @@
     - samtools/sort
   files:
     - path: output/samtools/test.sorted.bam
-      md5sum: 4adc495469724a375d5e1a9f3485e38d
+      md5sum: a73238d6b896a3a946025d6b13fe9525

tests/modules/samtools/stats/test.yml

@@ -5,7 +5,7 @@
     - samtools
   files:
     - path: output/samtools/test.paired_end.sorted.bam.stats
-      md5sum: 09146eeecfcae2a84fb8615c86cd8d64
+      md5sum: 6e3ca28b3e98dade14992dd7ea5fc886
 
 - name: samtools stats test_samtools_stats_cram
   command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
@@ -14,4 +14,4 @@
     - samtools
   files:
     - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
-      md5sum: ab49e7380714b7033e374ba1114e5e54
+      md5sum: 985455b573444c3743510d603ed41f8c