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quantms-utils 0.0.8 -> 0.0.9 #409

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Aug 17, 2024
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quantms-utils 0.0.8 -> 0.0.9 #409

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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Dependencies`

- quantms-utils==0.0.8
- quantms-utils==0.0.9
- diann==1.9.1

### `Parameters`
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6 changes: 3 additions & 3 deletions modules/local/add_sage_feat/main.nf
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Expand Up @@ -2,10 +2,10 @@ process SAGEFEATURE {
tag "$meta.mzml_id"
label 'process_low'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
tuple val(meta), path(id_file), path(extra_feat)
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6 changes: 3 additions & 3 deletions modules/local/diannconvert/main.nf
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Expand Up @@ -2,10 +2,10 @@ process DIANNCONVERT {
tag "$meta.experiment_id"
label 'process_medium'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
path(report)
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8 changes: 4 additions & 4 deletions modules/local/extract_psm/main.nf
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Expand Up @@ -2,17 +2,17 @@ process PSMCONVERSION {
tag "$meta.mzml_id"
label 'process_medium'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"


input:
tuple val(meta), path(idxml_file), path(spectrum_df)

output:
path "*_psm.csv", emit: psm_info
path "*_psm.parquet", emit: psm_info
path "versions.yml", emit: version
path "*.log", emit: log

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2 changes: 1 addition & 1 deletion modules/local/extract_psm/meta.yml
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Expand Up @@ -25,7 +25,7 @@ output:
- psm_info:
type: file
description: PSM csv file
pattern: "*_psm.csv"
pattern: "*_psm.parquet"
- version:
type: file
description: File containing software version
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6 changes: 3 additions & 3 deletions modules/local/generate_diann_cfg/main.nf
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Expand Up @@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
tag "$meta.experiment_id"
label 'process_low'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
val(meta)
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6 changes: 3 additions & 3 deletions modules/local/ms2rescore/main.nf
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Expand Up @@ -2,10 +2,10 @@ process MS2RESCORE {
tag "$meta.mzml_id"
label 'process_high'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

// userEmulation settings when docker is specified
containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
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6 changes: 3 additions & 3 deletions modules/local/mzmlstatistics/main.nf
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Expand Up @@ -3,10 +3,10 @@ process MZMLSTATISTICS {
label 'process_medium'
label 'process_single'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
tuple val(meta), path(ms_file)
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6 changes: 3 additions & 3 deletions modules/local/preprocess_expdesign.nf
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Expand Up @@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN {
tag "$design.Name"
label 'process_low'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
path design
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6 changes: 3 additions & 3 deletions modules/local/samplesheet_check.nf
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Expand Up @@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
tag "$input_file"
label 'process_single'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
path input_file
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6 changes: 3 additions & 3 deletions modules/local/sdrfparsing/main.nf
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Expand Up @@ -2,10 +2,10 @@ process SDRFPARSING {
tag "$sdrf.Name"
label 'process_low'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
path sdrf
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6 changes: 3 additions & 3 deletions modules/local/spectrum2features/main.nf
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Expand Up @@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
tag "$meta.mzml_id"
label 'process_low'

conda "bioconda::quantms-utils=0.0.8"
conda "bioconda::quantms-utils=0.0.9"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.8--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.8--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.9--pyhdfd78af_0' :
'biocontainers/quantms-utils:0.0.9--pyhdfd78af_0' }"

input:
tuple val(meta), path(id_file), path(ms_file)
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