Fix broken versions.yml file in last/train. #7393
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Here is the long story:
Escape sequences for newline and tab in a shell `tr` command were not
escaped in the script section of the module, causing them to be expanded
in `.command.sh`.
This did not prevent `tr` from doing its job, but this caused the lines
in the script to be indented, like this:
```
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2M:ALIGNMENT_TRAIN":
last: $(lastdb --version | sed 's/lastdb //')
END_VERSIONS
```
The indentation broke the herescript, but did not cause the module to
fail.
Therefore, the `versions.yml` file contained one extra line with
` END_VERSIONS` in it. This crashes the pipelines that collect the
version numbers, but this was not noticed because `last/train` is always
used with other `last/` submodules, and I was not using `last/train`'s
versions file until today, because I was assuming that the information
would always be redundant.
mashehu
approved these changes
Jan 30, 2025
11 tasks
charles-plessy
added a commit
to oist/LuscombeU_nfcore_pairgenomealign_fork
that referenced
this pull request
Jan 30, 2025
Also pull the fix for the versions channel of last/train (see <nf-core/modules#7393>)
|
"Unescaped Escape Sequences: A Silent Pipeline Failure" 😄 |
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Here is the long story:
Escape sequences for newline and tab in a shell
trcommand were not escaped in the script section of the module, causing them to be expanded in.command.sh.This did not prevent
trfrom doing its job, but this caused the lines in the script to be indented, like this:The indentation broke the herescript, but did not cause the module to fail.
Therefore, the
versions.ymlfile contained one extra line withEND_VERSIONSin it. This crashes the pipelines that collect theversion numbers, but this was not noticed because
last/trainis alwaysused with other
last/submodules, and I was not usinglast/train'sversions file until today, because I was assuming that the information
would always be redundant.
PR checklist
Closes #XXX
versions.ymlfile.labelnf-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