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Bump ms2rescore container with new timsTOF model #315

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merged 5 commits into from
Mar 12, 2024
Merged

Bump ms2rescore container with new timsTOF model #315

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069d0c0
bump ms2rescore container
jonasscheid Mar 8, 2024
1777864
try docker runoptions again
jonasscheid Mar 8, 2024
5b784e0
bump container build, previous had dependency issues
jonasscheid Mar 11, 2024
3811751
Merge branch 'bump-ms2rescore-container' of https://github.com/jonass…
jonasscheid Mar 11, 2024
142fb98
switch to container option
jonasscheid Mar 11, 2024
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2 changes: 1 addition & 1 deletion bin/ms2rescore_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@ def filter_out_artifact_psms(
"-o", "--output_path", help="Path and stem for output file names (default: derive from identification file)"
)
@click.option("-l", "--log_level", help="Logging level (default: `info`)", default="info")
@click.option("-n", "--processes", help="Number of parallel processes available to MS²Rescore", type=int, default=1)
@click.option("-n", "--processes", help="Number of parallel processes available to MS²Rescore", type=int, default=16)
@click.option("-f", "--fasta_file", help="Path to FASTA file")
@click.option(
"-fg",
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6 changes: 3 additions & 3 deletions modules/local/ms2rescore.nf
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Expand Up @@ -2,10 +2,10 @@ process MS2RESCORE {
tag "$meta.id"
label 'process_high'

conda "bioconda::ms2rescore=3.0.0"
conda "bioconda::ms2rescore=3.0.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ms2rescore:3.0.0--pyhdfd78af_0':
'biocontainers/ms2rescore:3.0.0--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/ms2rescore:3.0.1--pyhdfd78af_2':
'biocontainers/ms2rescore:3.0.1--pyhdfd78af_2' }"

// 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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