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Update immcantation container #296

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merged 2 commits into from
Jan 16, 2024
Merged

Update immcantation container #296

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2661370
update immcantation/airrflow container
ggabernet Jan 16, 2024
28cdf5b
update changelog
ggabernet Jan 16, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).

## [3.2.1dev] -
## [3.3.0dev] -

### `Added`

Expand All @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| multiqc | 1.14 | 1.18 |
| enchantr | 0.9.0 | 0.10.0 |

## [3.2.0] - 2023-10-27 Expecto patronum

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4 changes: 2 additions & 2 deletions modules/local/airrflow_report/airrflow_report.nf
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Expand Up @@ -6,8 +6,8 @@ process AIRRFLOW_REPORT {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
tuple val(meta), path(tab) // sequence tsv table in AIRR format
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4 changes: 2 additions & 2 deletions modules/local/enchantr/collapse_duplicates.nf
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Expand Up @@ -8,8 +8,8 @@ process COLLAPSE_DUPLICATES {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ]
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4 changes: 2 additions & 2 deletions modules/local/enchantr/define_clones.nf
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Expand Up @@ -25,8 +25,8 @@ process DEFINE_CLONES {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format
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4 changes: 2 additions & 2 deletions modules/local/enchantr/detect_contamination.nf
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Expand Up @@ -9,8 +9,8 @@ process DETECT_CONTAMINATION {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
path(tabs)
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4 changes: 2 additions & 2 deletions modules/local/enchantr/dowser_lineages.nf
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Expand Up @@ -25,8 +25,8 @@ process DOWSER_LINEAGES {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
tuple val(meta), path(tabs)
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4 changes: 2 additions & 2 deletions modules/local/enchantr/find_threshold.nf
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Expand Up @@ -25,8 +25,8 @@ process FIND_THRESHOLD {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"


input:
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4 changes: 2 additions & 2 deletions modules/local/enchantr/remove_chimeric.nf
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Expand Up @@ -9,8 +9,8 @@ process REMOVE_CHIMERIC {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"


input:
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4 changes: 2 additions & 2 deletions modules/local/enchantr/report_file_size.nf
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Expand Up @@ -10,8 +10,8 @@ process REPORT_FILE_SIZE {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
path logs
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4 changes: 2 additions & 2 deletions modules/local/enchantr/single_cell_qc.nf
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Expand Up @@ -24,8 +24,8 @@ process SINGLE_CELL_QC {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
path(tabs)
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4 changes: 2 additions & 2 deletions modules/local/enchantr/validate_input.nf
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Expand Up @@ -10,8 +10,8 @@ process VALIDATE_INPUT {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
file samplesheet
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4 changes: 2 additions & 2 deletions modules/local/reveal/add_meta_to_tab.nf
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Expand Up @@ -7,8 +7,8 @@ process ADD_META_TO_TAB {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

cache 'deep' // Without 'deep' this process would run when using -resume

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4 changes: 2 additions & 2 deletions modules/local/reveal/filter_junction_mod3.nf
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Expand Up @@ -7,8 +7,8 @@ process FILTER_JUNCTION_MOD3 {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
tuple val(meta), path(tab) // sequence tsv in AIRR format
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4 changes: 2 additions & 2 deletions modules/local/reveal/filter_quality.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ process FILTER_QUALITY {
error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/immcantation/airrflow:3.2.0':
'docker.io/immcantation/airrflow:3.2.0' }"
'docker.io/immcantation/airrflow:3.3.0':
'docker.io/immcantation/airrflow:3.3.0' }"

input:
tuple val(meta), path(tab) // sequence tsv in AIRR format
Expand Down