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nf-core modules update --all #420

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merged 3 commits into from
Aug 4, 2021
Merged

nf-core modules update --all #420

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0bcdd72
feat: nf-core modules update --all
maxulysse Aug 4, 2021
3812485
fix: code polishing
maxulysse Aug 4, 2021
abe359b
fix: revert to old tabix version
maxulysse Aug 4, 2021
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16 changes: 8 additions & 8 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -19,29 +19,29 @@
"git_sha": "c8877835c288eb32b2ad1810d38a78e83e791f3d"
},
"multiqc": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"samtools/faidx": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"samtools/merge": {
"git_sha": "adfb8a3d6541f363aec83df16df873cbb767b388"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"seqkit/split2": {
"git_sha": "65ab646870c4ff74322b4fff22ad51b190791a2c"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"snpeff": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
},
"tabix/bgziptabix": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"tabix/tabix": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
},
"trimgalore": {
"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
}
}
}
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/modules/multiqc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ process MULTIQC {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/multiqc:1.10.1--py_0"
container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/samtools/faidx/main.nf
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Expand Up @@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/samtools/merge/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,11 @@ process SAMTOOLS_MERGE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/seqkit/split2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,12 @@ process SEQKIT_SPLIT2 {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::seqkit=0.16.0" : null)
conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)

if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.0--h9ee0642_0"
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
} else {
container "quay.io/biocontainers/seqkit:0.16.0--h9ee0642_0"
container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/tabix/bgziptabix/main.nf
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Expand Up @@ -11,11 +11,11 @@ process TABIX_BGZIPTABIX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
} else {
container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/tabix/tabix/main.nf
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Expand Up @@ -11,11 +11,11 @@ process TABIX_TABIX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
} else {
container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
}

input:
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6 changes: 3 additions & 3 deletions modules/nf-core/modules/trimgalore/main.nf
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Expand Up @@ -11,11 +11,11 @@ process TRIMGALORE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
} else {
container "quay.io/biocontainers/trim-galore:0.6.6--0"
container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
}

input:
Expand Down