ENSGENOMIO-18 Chunking modules#34
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markquintontulloch wants to merge 45 commits into
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Dishalodha
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Partial review, will test the code when cluster is back.
Looks good overall, just minor updates.
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Leaving the update of the GenomIO container when the new version is released aside, looks good to me. A couple of suggestions and comments.
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| def args = [] | ||
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| if (params.chunk_id_regex) { | ||
| def rx = params.chunk_id_regex.replace("'", "'\"'\"'") | ||
| args << "--chunk-id-regex '${rx}'" | ||
| } | ||
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| if (params.allow_revcomp) { | ||
| args << "--allow-revcomp" | ||
| } | ||
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| def has_agp = agp && agp.baseName != 'NO_FILE' | ||
| if (has_agp) { | ||
| args << "--agp-file ${agp}" | ||
| } |
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Whilst I'm happy with using Nextflow's native language, I'm wondering how portable would this module be if we decided to move away from Nextflow compared to having this code in Bash inside the code block. In a way seeing this reminds me of our Perl code embedded inside eHive modules.
More a shared thought than an action to be made, honestly.
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Creating draft pull request as following changes required:
Container version for Genomio needs to be updated once python code approved, merged, and new release container created.
Tests need to be updated in accordance with group's new policy.Tests now updated to avoid use of stored files