Updates to modules -- should remove defaults #13
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muffato
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Dec 6, 2024
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CITATIONS.md, README.md, and docs/usage.md refer to Anaconda. Change as per https://sangertreeoflife.slack.com/archives/C02V3F79EMC/p1732526470246279
You've got to remove defaults from nextflow.config and subworkflows/nf-core/utils_nextflow_pipeline/main.nf.
How do you run tests ?
nextflow run /repo/ -profile test_full,sanger,singularity --outdir results
gives this error:
ERROR ~ No such variable: assembly_id
-- Check script 'repo/./workflows/../subworkflows/local/yaml_input.nf' at line: 14 or see '.nextflow.log' file for more details
(same problem on v0.6.1)
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All modules have now been updated, with the exception being SANGER-TOL-BTK as this would rely on upstream updates (if any are needed). Hopefully, the conda specific issues are solved here. Happy to wait on merge until we can also correct
any singularity issues too.
There is also a small change introduced to remove an if statement on an unnecessary "if haplotype exists..." hap will always exist, the statement just introduced more ambiguity.
This update will be followed by an update to the mapping subworkflow mentioned in #12