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idmapper changes #60

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merged 2 commits into from
Jan 28, 2022
Merged

idmapper changes #60

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0cee76b
sdrf -> 0.0.20
ypriverol Jan 28, 2022
7848717
sdrf -> 0.0.20
ypriverol Jan 28, 2022
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1 change: 0 additions & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ params {
}
'isobaricanalyzer' {
args = ''
publish_files = ['log': '']
}
'searchenginemsgf' {
args = ''
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1 change: 1 addition & 0 deletions modules/local/openms/idmapper/main.nf
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Expand Up @@ -38,6 +38,7 @@ process IDMAPPER {
-mz_tolerance $params.mz_tolerance \\
-mz_measure $params.mz_measure \\
-mz_reference $params.mz_reference \\
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you forgot to remove the old param

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and the docs/param description for it maybe too

-mz_reference 'precursor'
-debug 100 \\
-out ${id_file.baseName}_map.consensusXML \\
> ${id_file.baseName}_map.log
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6 changes: 3 additions & 3 deletions modules/local/samplesheet_check.nf
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Expand Up @@ -12,11 +12,11 @@ process SAMPLESHEET_CHECK {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.19" : null)
conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.20" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.18--pyhdfd78af_0"
container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.20--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/sdrf-pipelines:0.0.18--pyhdfd78af_0"
container "quay.io/biocontainers/sdrf-pipelines:0.0.20--pyhdfd78af_0"
}

input:
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8 changes: 4 additions & 4 deletions modules/local/sdrfparsing/main.nf
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Expand Up @@ -10,11 +10,11 @@ process SDRFPARSING {
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 ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.19" : null)
conda (params.enable_conda ? "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.20" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.18--pyhdfd78af_0"
container "https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.20--pyhdfd78af_0"
} else {
container "quay.io/biocontainers/sdrf-pipelines:0.0.18--pyhdfd78af_0"
container "quay.io/biocontainers/sdrf-pipelines:0.0.20--pyhdfd78af_0"
}

input:
Expand All @@ -36,6 +36,6 @@ process SDRFPARSING {

parse_sdrf $options.args -s ${sdrf} > sdrf_parsing.log

echo "0.0.19" > sdrf-pipelines.version.txt
echo "0.0.20" > sdrf-pipelines.version.txt
"""
}