Longread only functionality #718
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… 97 to 90 when dealing with longreads
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My pleasure hehe. Still WIP. I have to tidy up the code and run some validation on real data, but we're getting there! |
…rtread assemblers, when assembly input is given
…empty if no files are given
…d also return remainder in case the ch_short_reads channel is empty. Change config for FILTLONG to only use '--trim' option if shortreads are passed
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So far in this PR I have
Downstream from the assembly, except for the binning preparation, the long read and short read assemblies are treated the same. |
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Me and some colleagues are running some tests on ont data, and I think this works as expected. We will continue testing and play around with the parameters, but if anyone wants to have a look through the code and suggest improvements, that would be awesome! |
| BOWTIE2_ASSEMBLY_BUILD ( assemblies ) | ||
| ch_versions = Channel.empty() | ||
| ch_multiqc_files = Channel.empty() | ||
| // multiple symlinks to the same assembly -> use first of sorted list |
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| // multiple symlinks to the same assembly -> use first of sorted list | |
| // multiple symlinks to the same assembly -> use first of sorted list |
What is this comment referring to, it sounds a bit scary?
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Did a lot of copy-pasting here from original binning_preparation.nf, forgot to remove this comment :) the comment is referring to line 47 in shortread_binning_preparation.nf if you are interest. I did not write this line of code though.
| ch_minimap2_input_idx = ch_minimap2_input | ||
| .map { meta_idx, index, meta, reads -> [ meta_idx, index ] } | ||
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| MINIMAP2_ASSEMBLY_ALIGN ( ch_minimap2_input_reads, ch_minimap2_input_idx, true, 'bai', false, false ) |
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What are the true/false/falses? something should be parameterasable by the user?
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first true: if the output should be in bam-format. I think this can be fixed
first false: If the output is set to paf, then a cigar string is generated. This only happens if output format is not bam, so does not make sense for it to be changed by user
second false: to make the cigar string backward compatible with older tools, but no need for that here.
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thank you @jfy133. I'm away this week, but I'll try to find time to go through your comments asap. |
Co-authored-by: James A. Fellows Yates <[email protected]>
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Thanks for the review @jfy133. Sorry I have been away this week, but now I think I addressed all of your comments. |
This PR adds long-read only functionality to mag.
closes #662, #659, #275
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).