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Fix docker container permissions for ms2rescore #302

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merged 7 commits into from
Feb 19, 2024
Merged

Fix docker container permissions for ms2rescore #302

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f30c2b6
change to docker process.containerOptions, fix percolator test profile
jonasscheid Jan 23, 2024
065e324
add flags that have been set by userEmulation previously
jonasscheid Jan 23, 2024
9bc32e3
pin prettier version to pass linting
jonasscheid Jan 23, 2024
0af6d95
try former userEmulation settings in docker.runOptions
jonasscheid Jan 29, 2024
5067217
Revisit attempt via process.containerOptions
jonasscheid Jan 29, 2024
447bba5
fix typo
jonasscheid Feb 16, 2024
f34ebc7
merge dev into feature branch
jonasscheid Feb 16, 2024
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1 change: 1 addition & 0 deletions conf/modules.config
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Expand Up @@ -157,6 +157,7 @@ process {
}

withName: 'MS2RESCORE' {
containerOptions = '-u $(id -u) -e "HOME=${HOME}" -v $HOME:$HOME'
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Does this work like this or does it need to be process.containerOptions?

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process.containerOptions works only in the nextflow.config

I oriented myself by Julia's fix: nf-core/tools#2673

By this we can define container options on module level, that is not possible with runOptions

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And: The MS2Rescore container needed a specific "treatment" in order to run, else permission issues. Previously that was handled by userEmulation, but that is/will be removed :/

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Ok so this works when having sudo rights, but apparently not via GH actions.. Im gonna test the full diff compared to userEmulation

ext.args = [
"--ms2_tolerance ${2 * params.fragment_mass_tolerance}",
"--ms2pip_model ${params.ms2pip_model}",
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2 changes: 1 addition & 1 deletion conf/test_percolator.config
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Expand Up @@ -25,5 +25,5 @@ params {

// Don't do quantification since this step needs a larger test dataset (-> test quantification using test_full)
skip_quantification = true
rescoring_engine = 'mokapot'
rescoring_engine = 'percolator'
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}
18 changes: 9 additions & 9 deletions nextflow.config
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Expand Up @@ -161,17 +161,17 @@ profiles {
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = ''
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
process.containerOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '--platform=linux/amd64'
process.containerOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
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