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Getting mapped bam and bai published in the same folder #1541

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merged 5 commits into from
May 27, 2024
Merged

Getting mapped bam and bai published in the same folder #1541

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66ecfb2
Using meta.sample for meta.id in channel reads_for_alignment when met…
asp8200 May 23, 2024
6f3c450
Updating changelog
asp8200 May 23, 2024
8d1592c
prettier
asp8200 May 23, 2024
8e2d82a
Merge branch 'dev' into fix_1540
asp8200 May 27, 2024
01fe57d
fixing changelog
asp8200 May 27, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

- [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
- [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`

### Removed
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6 changes: 6 additions & 0 deletions workflows/sarek/main.nf
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Expand Up @@ -253,6 +253,12 @@ workflow SAREK {
}
.set { reads_grouping_key }

reads_for_alignment = reads_for_alignment.map{ meta, reads ->
// Update meta.id to meta.sample no multiple lanes or splitted fastqs
if (meta.size * meta.num_lanes == 1) [ meta + [ id:meta.sample ], reads ]
else [ meta, reads ]
}

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can this not be moved up to the previous mapping statement?

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Not sure what you mean, but you're welcome to move stuff around.

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Never mind, the other is Adam's cool grouping logic. One more concern from my side, below there is the joining between the reads_grouping_key and reads_alignment meta's. Is this working for both splitting and unsplitting and across several lanes?

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No idea 😬

You mean these combine-statements:

https://github.com/asp8200/sarek/blob/8d1592c242fbb2bd2cc7da66377032d55afc7816/workflows/sarek/main.nf#L270

https://github.com/asp8200/sarek/blob/8d1592c242fbb2bd2cc7da66377032d55afc7816/workflows/sarek/main.nf#L288

I just hope we have CI-tests covering all this intricate stuff 🤞

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#1544

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How about we merge as is for now, and we'll take care of beautifying it when we refactor?

// reads will be sorted
sort_bam = true
FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON(reads_for_alignment, index_alignment, sort_bam, fasta, fasta_fai)
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