fix container definition formatting for fgumi/gatk4 - #12756
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you can force merge this one and skip CI to save the polar bear forest
mashehu
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`nf-core modules bump-versions` rewrote the container directive with the
ternary operators at column 0 and padding inside `${...}`:
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://...'
: 'quay.io/...' }"
Every module in nf-core/modules writes the operators at the start of the
indented continuation lines instead, with no padding:
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://...'
: 'quay.io/...'}"
The cause is the order of the interpolations in `_replace`: `f"? {inner_indent}"`
emits the operator before the indent rather than after it.
This is the formatting undone by hand across 106 files in nf-core/modules#12756,
which is the PR the issue links to.
Adds a regression test asserting the canonical block is what lands in main.nf.
Closes nf-core#4452
Signed-off-by: Ashar Ali <aaa467@njit.edu>
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PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda