trying to fix the concatenation of fastq files #46
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@ramprasadn, would very much appreciate your thoughts on this PR :) |
Lucpen
reviewed
Oct 31, 2023
Comment on lines
+105
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| def branchFastqToSingleAndMulti(ch_reads) { | ||
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| return ch_reads | ||
| .map { | ||
| meta, fastq -> | ||
| original_id = meta.id.split('_T')[0..-2].join('_') | ||
| [ meta + [id: original_id], fastq ] | ||
| } | ||
| .groupTuple() | ||
| .branch { | ||
| meta, fastq -> | ||
| single_fq: fastq.size() == 1 | ||
| return [ meta, fastq.flatten() ] | ||
| multiple_fq: fastq.size() > 1 | ||
| return [ meta, fastq.flatten() ] | ||
| } | ||
| } |
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It´s true, it would concatenate all the time as it is written.
They do like this in RNAseq. It is pretty much the same as you have done, but what if sample id does not end in _T? Could we instead ask for input fastq from R1 to be separated by " "?
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We could think of changing the T to something else. Right now it is added to the sample name in this function.
tomte/bin/check_samplesheet.py
Line 147 in ac85767
So the sample name will always have this suffix. When we switch to nf-validation we can change this :)
Lucpen
approved these changes
Oct 31, 2023
ramprasadn
reviewed
Oct 31, 2023
Comment on lines
+116
to
+119
| single_fq: fastq.size() == 1 | ||
| return [ meta, fastq.flatten() ] | ||
| multiple_fq: fastq.size() > 1 | ||
| return [ meta, fastq.flatten() ] |
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Is branching needed here? Asking because the returned output looks the same for both branches.
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We feed the multiple branch into the cat CAT process and then mix it later. They should not be the same 😅
This is mostly taken from the rna fusion pipeline which has taken the code from the rnaseq pipe.
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ramprasadn
approved these changes
Oct 31, 2023
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When running tomte with samples having multiple fastq pairs linked to them, Tomte wasn't able to concatenate fastq files belonging to the same sample. This should fix that issue
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).