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[ENH] Add profile full_pipeline + fix stubrun #98

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[ENH] Add profile full_pipeline + fix stubrun #98

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c365f18
add profile full_pipeline + another way to run stubrun
arnaudbore Mar 26, 2026
6a5b5aa
fix profile for test
arnaudbore Mar 26, 2026
e63d92d
fix stubrun profile in test
arnaudbore Mar 26, 2026
c780ca3
fix action
arnaudbore Mar 26, 2026
ef8b0d8
update stubrun + config bundleseg
arnaudbore Mar 26, 2026
d463ae8
fix ascii and profiles
arnaudbore Mar 27, 2026
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2 changes: 1 addition & 1 deletion .github/actions/nf-test/action.yml
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Expand Up @@ -62,7 +62,7 @@ runs:
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
run: |
nf-test test \
--profile=+${{ inputs.profile }} \
--profile=+${{ inputs.profile }}, stubRun \
$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
--ci \
--changed-since HEAD^ \
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1 change: 0 additions & 1 deletion conf/modules.config
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Expand Up @@ -27,4 +27,3 @@ includeConfig './modules/tractometry.config'
includeConfig './modules/harmonization.config'
includeConfig './modules/output_orig_space.config'
includeConfig './modules/output_template_space.config'
includeConfig './modules/stubrun.config'
3 changes: 3 additions & 0 deletions conf/reproducible.config
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Expand Up @@ -11,4 +11,7 @@
*/

process {
withName: '.*' {
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@levje levje Mar 26, 2026

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What is this for? Some tasks will probably fail with a single CPU.

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@AlexVCaron AlexVCaron Mar 27, 2026

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It's also not specific. Following docs, it falls off behind all other selectors. Report if it's cornering use-cases correctly. From my gist, this gets applied if no other config gets loaded

cpus = 1
}
}
3 changes: 3 additions & 0 deletions nextflow.config
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Expand Up @@ -415,6 +415,9 @@ profiles {
skip_preproc {
includeConfig 'conf/skip_preproc.config'
}
stubRun {
includeConfig 'conf/modules/stubrun.config'
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
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