Dev #89
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Dev #89
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@mirpedrol Thank you for the quick response. I pulled upstream template and merged by And then fixed the collision. Did I missed anything? |
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That should work. I was looking at it again, and it might be due to some merge conflicts you had, for example you define the |
Thank you for point that out. I removed the duplicated lines. |
mirpedrol
reviewed
Jul 12, 2023
subworkflows/local/input_check.nf
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| .csv | ||
| .splitCsv ( header:true, sep:',' ) | ||
| .map { create_fastq_channel(it) } | ||
| Channel.fromSamplesheet("input") |
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This is working fine, so my comment is only a suggestion. You can remove the whole input_check subworkflow by creating the input channel in the main script. If you want to see an example, rnaseq has a PR with these changes.
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I tried but I have trouble in appending the meta.id by map with pseudo-code:
.map{
meta, fq1, fq2 ->
meta.id = meta.group + "_REP" + meta.replicate + "_T" + meta.techniquerep // I have trouble here
[meta, [fq1, fq2]]
}
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This is modifying the meta map in place, which can lead to errors in the pipeline. An alternative is using the operators + or - which create a copy of the object instead.
meta - meta.subMap('id') + [id: meta.group + "_REP" + meta.replicate + "_T" + meta.techniquerep
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I removed the input_check.nf. Could you please take a second look?
mirpedrol
approved these changes
Jul 13, 2023
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to
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| if (!params.gtf && !params.gff) { | ||
| Nextflow.error("No GTF or GFF3 annotation specified! The pipeline requires at least one of these files.") |
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Do you have params.gtf and params.gff? I can't see them in nextflow.config
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They are appended the main.nf.
workflows/hicar.nf
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| meta.group = meta.group.toString().replaceAll("\\.", "_") | ||
| meta - meta.subMap(['id', 'single_end']) + [id: meta.group + "_REP" + meta.replicate + "_T" + meta.techniquereplicate, single_end: false] |
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Suggested change
| meta.group = meta.group.toString().replaceAll("\\.", "_") | |
| meta - meta.subMap(['id', 'single_end']) + [id: meta.group + "_REP" + meta.replicate + "_T" + meta.techniquereplicate, single_end: false] | |
| meta.group = meta.group.toString().replaceAll("\\.", "_") | |
| meta - meta.subMap(['id', 'single_end', 'group']) + [id: meta.group + "_REP" + meta.replicate + "_T" + meta.techniquereplicate, single_end: false, 'group': meta.group.toString().replaceAll("\\.", "_")] |
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PR checklist
nf-core lint).nextflow run . -profile 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).