Samtools version update (#1507)

* Fix typo * update version to 1.15.1 * Fix md5sums * update mulled containers * update md5sums * update md5sums
2024-11-13 05:13:09 +00:00 · 2022-04-11 14:26:28 +02:00 · 2022-04-11 14:26:28 +02:00 · 897c33d5da
commit 897c33d5da
parent 8dc680d3b3
41 changed files with 105 additions and 112 deletions
--- a/modules/bbmap/align/main.nf
+++ b/modules/bbmap/align/main.nf
@ -2,10 +2,10 @@ process BBMAP_ALIGN {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
+    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
-        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' :
+        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }"

    input:
    tuple val(meta), path(fastq)
--- a/modules/bbmap/pileup/main.nf
+++ b/modules/bbmap/pileup/main.nf
@ -2,10 +2,10 @@ process BBMAP_PILEUP {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
+    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
-        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' :
+        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/bowtie/align/main.nf
+++ b/modules/bowtie/align/main.nf
@ -2,10 +2,10 @@ process BOWTIE_ALIGN {
    tag "$meta.id"
    label 'process_high'

-    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.11' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' :
-        'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' :
+        'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@ -2,10 +2,10 @@ process BOWTIE2_ALIGN {
    tag "$meta.id"
    label 'process_high'

-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
+        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/bwa/mem/main.nf
+++ b/modules/bwa/mem/main.nf
@ -2,10 +2,10 @@ process BWA_MEM {
    tag "$meta.id"
    label 'process_high'

-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/bwa/sampe/main.nf
+++ b/modules/bwa/sampe/main.nf
@ -2,10 +2,10 @@ process BWA_SAMPE {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"

    input:
    tuple val(meta), path(reads), path(sai)
--- a/modules/bwa/samse/main.nf
+++ b/modules/bwa/samse/main.nf
@ -2,10 +2,10 @@ process BWA_SAMSE {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"

    input:
    tuple val(meta), path(reads), path(sai)
--- a/modules/bwamem2/mem/main.nf
+++ b/modules/bwamem2/mem/main.nf
@ -2,10 +2,10 @@ process BWAMEM2_MEM {
    tag "$meta.id"
    label 'process_high'

-    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' :
-        'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' :
+        'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/chromap/chromap/main.nf
+++ b/modules/chromap/chromap/main.nf
@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' :
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/dragmap/align/main.nf
+++ b/modules/dragmap/align/main.nf
@ -2,10 +2,10 @@ process DRAGMAP_ALIGN {
    tag "$meta.id"
    label 'process_high'

-    conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.14 conda-forge::pigz=2.3.4" : null)
+    conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0':
-        'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0':
+        'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/hisat2/align/main.nf
+++ b/modules/hisat2/align/main.nf
@ -4,10 +4,10 @@ process HISAT2_ALIGN {
    tag "$meta.id"
    label 'process_high'

-    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' :
-        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' :
+        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/qualimap/bamqccram/main.nf
+++ b/modules/qualimap/bamqccram/main.nf
@ -2,10 +2,10 @@ process QUALIMAP_BAMQCCRAM {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' :
-        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' :
+        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' }"

    input:
    tuple val(meta), path(cram), path(crai)
--- a/modules/samblaster/main.nf
+++ b/modules/samblaster/main.nf
@ -2,10 +2,10 @@ process SAMBLASTER {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' :
-        'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' :
+        'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_AMPLICONCLIP {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/bam2fq/main.nf
+++ b/modules/samtools/bam2fq/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(inputbam)
--- a/modules/samtools/depth/main.nf
+++ b/modules/samtools/depth/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_DEPTH {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX {
    tag "$fasta"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(fasta)
--- a/modules/samtools/fastq/main.nf
+++ b/modules/samtools/fastq/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_FIXMATE {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam), path(bai)
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam), path(bai)
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(input)
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_MERGE {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(input_files)
--- a/modules/samtools/mpileup/main.nf
+++ b/modules/samtools/mpileup/main.nf
@ -2,11 +2,10 @@ process SAMTOOLS_MPILEUP {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
-
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
    input:
    tuple val(meta), path(input), path(intervals)
    path  fasta
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
    tag "$meta.id"
    label 'process_low'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(input), path(input_index)
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@ -2,10 +2,10 @@ process SAMTOOLS_VIEW {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

    input:
    tuple val(meta), path(input)
--- a/modules/star/genomegenerate/main.nf
+++ b/modules/star/genomegenerate/main.nf
@ -3,10 +3,10 @@ process STAR_GENOMEGENERATE {
    label 'process_high'

    // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.13 conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0' :
-        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' :
+        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' }"

    input:
    path fasta
--- a/modules/yara/mapper/main.nf
+++ b/modules/yara/mapper/main.nf
@ -2,10 +2,10 @@ process YARA_MAPPER {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' :
-        'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' :
+        'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' }"

    input:
    tuple val(meta), path(reads)
--- a/tests/modules/bbmap/align/test.yml
+++ b/tests/modules/bbmap/align/test.yml
@ -5,7 +5,7 @@
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
-      md5sum: e0ec7f1eec537acf146fac1cbdd868d1
+      md5sum: 8549040067d23949bddb6fe2ad211c92
    - path: output/bbmap/test.bbmap.log

 - name: bbmap align paired end index ref
@ -15,7 +15,7 @@
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
-      md5sum: 345a72a0d58366d75dd263b107caa460
+      md5sum: aeb842491ca6c7806aa7103b5223620f
    - path: output/bbmap/test.bbmap.log

 - name: bbmap align single end index ref
@ -25,7 +25,7 @@
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
-      md5sum: 95f690636581ce9b27cf8568c715ae4d
+      md5sum: b6a41cb344a343d46244d8f94eb66ec0
    - path: output/bbmap/test.bbmap.log

 - name: bbmap align paired end index ref pigz
@ -35,5 +35,5 @@
    - bbmap/align
  files:
    - path: output/bbmap/test.bam
-      md5sum: 441c4f196b9a82c7b224903538064308
+      md5sum: 74944e24acccb8c5abc316dcdd623c84
    - path: output/bbmap/test.bbmap.log
--- a/tests/modules/bbmap/pileup/test.yml
+++ b/tests/modules/bbmap/pileup/test.yml
@ -9,4 +9,4 @@
    - path: "output/bbmap/test.coverage.hist.txt"
      md5sum: 96915920ef42ddc9483457dd4585a088
    - path: output/bbmap/versions.yml
-      md5sum: 894acc38bdc167dc22851df15e5a8453
+      md5sum: e2bc51873b24e7fea269b7c1501de060
--- a/tests/modules/bwa/sampe/test.yml
+++ b/tests/modules/bwa/sampe/test.yml
@ -5,4 +5,4 @@
    - bwa/sampe
  files:
    - path: output/bwa/test.bam
-      md5sum: 01d1d71c88b6de07ed51d1d06e9e970b
+      md5sum: 67528d633a1a78e3d0e8d1486c1a960a
--- a/tests/modules/bwa/samse/test.yml
+++ b/tests/modules/bwa/samse/test.yml
@ -5,4 +5,4 @@
    - bwa/samse
  files:
    - path: output/bwa/test.bam
-      md5sum: ddfa4a8f6b65d44704a2d9528abc7e79
+      md5sum: 9a0ca9678a03e6fa4bda459c04c99bd6
--- a/tests/modules/chromap/chromap/test.yml
+++ b/tests/modules/chromap/chromap/test.yml
@ -8,7 +8,6 @@
    - path: output/chromap/test.bed.gz
      md5sum: 25e40bde24c7b447292cd68573728694
    - path: output/chromap/versions.yml
-      md5sum: d24cfc35ad958206a5bc5694221b4fae

 - name: chromap chromap test_chromap_chromap_paired_end
  command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -20,7 +19,6 @@
    - path: output/chromap/test.bed.gz
      md5sum: 7cdc8448882b75811e0c784f5f20aef2
    - path: output/chromap/versions.yml
-      md5sum: 68ffe268a9d460956de4aad2a55ffd68

 - name: chromap chromap test_chromap_chromap_paired_bam
  command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -30,6 +28,5 @@
  files:
    - path: output/chromap/genome.index
    - path: output/chromap/test.bam
-      md5sum: df467417407408e42992dc3dd15b22f5
+      md5sum: 0cb45628d1abe4b4359650040c501aef
    - path: output/chromap/versions.yml
-      md5sum: ea732b4c6f1312d09745b66c3963dd3f
--- a/tests/modules/samblaster/test.yml
+++ b/tests/modules/samblaster/test.yml
@ -4,4 +4,4 @@
    - samblaster
  files:
    - path: output/samblaster/test.processed.bam
-      md5sum: 950f23d85f75be1cf872f45c0144bdf4
+      md5sum: 3009528be9f69e7fc8951921583b0016
--- a/tests/modules/samtools/ampliconclip/test.yml
+++ b/tests/modules/samtools/ampliconclip/test.yml
@ -5,7 +5,7 @@
    - samtools/ampliconclip
  files:
    - path: output/samtools/test.bam
-      md5sum: 5d0e8bc9e6059ef3a63ee6328a3935c7
+      md5sum: d270363a7fb3d96be2df211099efc75b

 - 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: 2c998295d624c59620b7ffdb0cc080e2
+      md5sum: e7c4e64c259212e1670f6de96a5549b4
    - path: output/samtools/test.cliprejects.bam
-      md5sum: f3ebba8d91ad29cc4d2d00943e6f6bab
+      md5sum: b7c057b11950c2271a0c92236bee94b7

 - 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: 87882973b425ab27aad6ef18faf11f25
+      md5sum: e75992d4ff69cbaed9a089231be86b5e
    - path: output/samtools/test.cliprejects.bam
-      md5sum: eb5e186e1a69864dc2e99a290f02ff78
+      md5sum: 729f03e7a2801d2c56c32bef8f3d6ead
    - path: output/samtools/test.clipstats.txt
      md5sum: fc23355e1743d47f2541f2cb1a7a0cda
--- a/tests/modules/samtools/faidx/test.yml
+++ b/tests/modules/samtools/faidx/test.yml
@ -7,4 +7,3 @@
    - path: output/samtools/genome.fasta.fai
      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
    - path: output/samtools/versions.yml
-      md5sum: 6a16b2148a0ab43e6d0506056e6a0409
--- a/tests/modules/samtools/fixmate/test.yml
+++ b/tests/modules/samtools/fixmate/test.yml
@ -5,4 +5,4 @@
    - samtools/fixmate
  files:
    - path: output/samtools/test.bam
-      md5sum: c7f574bb0c469e0ccfecb6b7210e03c5
+      md5sum: 13805ea1a9212496a8cb4ce395b25119
--- a/tests/modules/samtools/mpileup/test.yml
+++ b/tests/modules/samtools/mpileup/test.yml
@ -7,7 +7,6 @@
    - path: output/samtools/test.mpileup
      md5sum: 958e6bead4103d72026f80153b6b5150
    - path: output/samtools/versions.yml
-      md5sum: 26350e1e145451f0b807911db029861e

 - name: samtools mpileup test_samtools_mpileup_intervals
  command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup_intervals -c tests/config/nextflow.config
@ -18,4 +17,3 @@
    - path: output/samtools/test.mpileup
      md5sum: 958e6bead4103d72026f80153b6b5150
    - path: output/samtools/versions.yml
-      md5sum: 11d8118a558efb9db6798453862d719c
--- a/tests/modules/samtools/sort/test.yml
+++ b/tests/modules/samtools/sort/test.yml
@ -5,4 +5,4 @@
    - samtools/sort
  files:
    - path: output/samtools/test.sorted.bam
-      md5sum: a73238d6b896a3a946025d6b13fe9525
+      md5sum: f00f5d392fd5c531e1fd528d9f57b32b
--- a/tests/modules/samtools/stats/test.yml
+++ b/tests/modules/samtools/stats/test.yml
@ -5,7 +5,7 @@
    - samtools
  files:
    - path: output/samtools/test.paired_end.sorted.bam.stats
-      md5sum: 6e3ca28b3e98dade14992dd7ea5fc886
+      md5sum: c1e9ad551281b0bca32be1c832d125af

 - 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: 985455b573444c3743510d603ed41f8c
+      md5sum: 103cd7b19743c42dab9ce570144c6f36