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should I pump the version of the failed tools in the collection? |
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No, thats not needed |
bernt-matthias
added
the
skip-version-check
| <inputs> | ||
| <param name="input" type="data" format="sam,bam,cram" label="Input File"/> | ||
| <section name="advanced_options" title="Advanced Options" expanded="no"> | ||
| <param name="add_pg" type="boolean" label="Add @PG in Header" checked="true" truevalue="" falsevalue="--no-PG" help="Add a @PG line to the header of the output file. "/> |
tool_collections/samtools/samtools_collate/samtools_collate.xml
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tool_collections/samtools/samtools_collate/samtools_collate.xml
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!!! Still need to restrict output to BAM format!!!
bgruening
reviewed
Feb 14, 2026
| $fast_mode | ||
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| $input | ||
| -o $output_file |
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all input data or output data should be single-quoted
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FOR CONTRIBUTOR:
There are two labels that allow to ignore specific (false positive) tool linter errors:
skip-version-check: Use it if only a subset of the tools has been updated in a suite.skip-url-check: Use it if github CI sees 403 errors, but the URLs work.