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Updating to samtools v1.19.2 #4907

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merged 3 commits into from
Feb 13, 2024
Merged

Updating to samtools v1.19.2 #4907

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9910129
Updating to samtools v1.19.2
asp8200 Feb 13, 2024
5e41849
Updating snapshots
asp8200 Feb 13, 2024
ed1d516
Also fixing snapshots of subworkflows using samtools
asp8200 Feb 13, 2024
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4 changes: 2 additions & 2 deletions modules/nf-core/samtools/ampliconclip/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::samtools=1.18
- bioconda::htslib=1.18
- bioconda::samtools=1.19.2
- bioconda::htslib=1.19.1
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/ampliconclip/main.nf
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Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_AMPLICONCLIP {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
'biocontainers/samtools:1.18--h50ea8bc_1' }"
'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
'biocontainers/samtools:1.19.2--h50ea8bc_0' }"

input:
tuple val(meta), path(bam)
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138 changes: 95 additions & 43 deletions modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap
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4 changes: 2 additions & 2 deletions modules/nf-core/samtools/bam2fq/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::samtools=1.18
- bioconda::htslib=1.18
- bioconda::samtools=1.19.2
- bioconda::htslib=1.19.1
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/bam2fq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_BAM2FQ {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
'biocontainers/samtools:1.18--h50ea8bc_1' }"
'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
'biocontainers/samtools:1.19.2--h50ea8bc_0' }"

input:
tuple val(meta), path(inputbam)
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12 changes: 6 additions & 6 deletions modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
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4 changes: 2 additions & 2 deletions modules/nf-core/samtools/calmd/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::samtools=1.18
- bioconda::htslib=1.18
- bioconda::samtools=1.19.2
- bioconda::htslib=1.19.1
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/calmd/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_CALMD {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
'biocontainers/samtools:1.18--h50ea8bc_1' }"
'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
'biocontainers/samtools:1.19.2--h50ea8bc_0' }"

input:
tuple val(meta), path(bam)
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-core/samtools/calmd/tests/main.nf.test.snap
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4 changes: 2 additions & 2 deletions modules/nf-core/samtools/cat/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::samtools=1.18
- bioconda::htslib=1.18
- bioconda::samtools=1.19.2
- bioconda::htslib=1.19.1
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/cat/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_CAT {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
'biocontainers/samtools:1.18--h50ea8bc_1' }"
'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
'biocontainers/samtools:1.19.2--h50ea8bc_0' }"

input:
tuple val(meta), path(input_files, stageAs: "?/*")
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