Update modules #449
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Update modules #449
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jemten
reviewed
Nov 23, 2023
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Looks good, just a comment about the names of the channel branches. It took me a couple of minutes to figure out which branch was what. Or maybe that is as easy as it will get. Also, the svdb_query prefix which should not cause any issues for now but is a potential headache.
| @@ -13,7 +13,8 @@ process SVDB_QUERY { | |||
| val(in_frqs) | |||
| val(out_occs) | |||
| val(out_frqs) | |||
| path (vcf_dbs) | |||
| path(vcf_dbs) | |||
| path(bedpe_dbs) | |||
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| output: | |||
| tuple val(meta), path("*_query.vcf") , emit: vcf | |||
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Just realising that this module is dependent on the user/developer setting ext.prefixto something like `${meta.id}_svdbquery. Failing to do this it won't work. Either the module needs to be hardcoded to add that prefix or the output needs to change to use ${prefix}.vcf. Or have I missed something?
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SVDB's output carries that suffix by default https://github.com/J35P312/SVDB/blob/c8c538089fd5f05d891db3686d83a79c97d5adbf/svdb/__main__.py#L32
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Lucpen
reviewed
Nov 23, 2023
| @@ -4,7 +4,7 @@ process EKLIPSE { | |||
| label 'process_single' | |||
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| // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. | |||
| conda "bioconda::eklipse=1.8" | |||
| conda "${moduleDir}/environment.yml" | |||
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Very nice, now the environment is directly there. Is it like that for all the new modules?
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Yupe.. with nf-tests every tool and subtool will come as a unit containing scripts, tests, and the environment :)
jemten
approved these changes
Nov 24, 2023
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Looks good! Could you just check that SVDB_query works as intended when you run both a vcf and bedpe database. Right now they will have the same suffix and I don't know which file be selected to the emit channel. Go ahead and merge when you feel confident in the code
…edisease into smallupdates
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PR checklist
This PR updates two modules (eklipse & svdb query) and introduces along relevant changes in the pipeline.
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).