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Joon-Klaps
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Joon-Klaps
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Very nice work, no major comments. Only suggestions.
| make_dir(out_dir) | ||
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| ## Create list of fastq-scan json files | ||
| json_files = sorted(glob.glob('*.json')) |
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nitpicking
I think it would be better if you were to ask for an input dir in args and search there for json files instead of working dir.
| raw_json_files = sorted(glob.glob('*.raw.json')) | ||
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| ## Create list of processed reads fastq-scan json files | ||
| processed_json_files = sorted(glob.glob('*.processed.json')) |
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nitpicking... again sorry
Same here, think it would be better if you were to ask for input params & use in nextflow the stageAs.
| { assert snapshot( | ||
| process.out.vcf.collect { file(it[1]).getName() }, | ||
| process.out.tbi.collect { file(it[1]).getName() }, | ||
| process.out.versions, | ||
| process.out.phased_vcf.collect { file(it[1]).getName() }, | ||
| process.out.phased_tbi.collect { file(it[1]).getName() }).match()} | ||
| ) |
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I'm guessing it's not stable due to the vcf header?
Might be interesting to use nft-vcf plugin with it's function .variantsMD5
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I'm not sure how to address this. This was the original main.nf.test from nf-core.
| process.out.phased_vcf.collect { file(it[1]).getName() }, | ||
| process.out.phased_tbi.collect { file(it[1]).getName() }).match()} |
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phased_vcf & phased_tbi their names are not stored in snapshot. It's an empty array.
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I'm not sure how to address this. This was the original main.nf.test from nf-core.
post pre-release review
update template files
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).