chore: release 1.0.1 #70
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Co-authored-by: Maxime U Garcia <[email protected]>
Fixes a bug where alignment and filtering where swapped in the phase 2 high-throughput diagrams. Thanks James Fellows Yates (@jfy133)
updates post 1.0.0 release
Add when conditions to prepare
Allow escalation of memory for FilterConsensusReads
comma-delimited string Fixes #62
Co-authored-by: Nils Homer <[email protected]>
There's a bug in `samtools merge --template-coordinate' that causes the output not to be correctly sorted. Here, we re-sort via fgbio SortBam to ensure the output is properly sorted. fgbio SortBam can be removed when the fix to the samtools bug is released. See: samtools/samtools#2062
Co-authored-by: Simon Pearce <[email protected]>
Allow igenomes to work
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Add stubs to all local modules
clintval
approved these changes
Sep 9, 2024
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| // MODULE: Run fgbio SortBam to re-sort into TemplateCoordinate. This can be removed when samtools is released | ||
| // with the following bugfix: https://github.com/samtools/samtools/pull/2062 | ||
| // | ||
| SORTBAM(MERGE_BAM.out.bam) |
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This is unfortunate because it will probably create a performance/speed regression but I do see we can move off it once a new samtools release is made!
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Yes, it isn't ideal but better than a non-functional pipeline.
chore: correct date
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1.0.1 Release PR
Note the "Test successful pipeline download with 'nf-core download'" actions are failing (and have always failed) due to a memory error, but the pipeline is downloaded successfully. It might be worth fixing this properly for the next release.
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).