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CSI bam index not working #327

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heathfuqua opened this issue Aug 10, 2023 · 1 comment · Fixed by #328
Open

CSI bam index not working #327

heathfuqua opened this issue Aug 10, 2023 · 1 comment · Fixed by #328
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@heathfuqua
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Description of the bug

With large genomes, the .bai index file format is insufficient so .csi file format is specified by "ext.args='-c'" in SAMTOOLS_INDEX.
The pipeline first fails with a docker timeout error. Upon -resume it completes "without errors" but skips most processes.

FASTQ_ALIGN_BWA can output .csi file but lines 165-177 of atacseq.nf seems to only allow .bai in ch_genome_bam_index.

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Relevant files

Archive.zip

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@heathfuqua heathfuqua added the bug Something isn't working label Aug 10, 2023
@bjlang bjlang linked a pull request Aug 11, 2023 that will close this issue
Add consistent support of .csi indices as alternative to .bai #328
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bjlang commented Aug 11, 2023

Fixed in #328

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Add consistent support of .csi indices as alternative to .bai bjlang/nf-core-atacseq
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@heathfuqua @bjlang