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The reason that pinaplpy does not find any successful reads is because it prioritises the .sam files over .bam files. I've changed the code a bit to fix the issue temporarily (very sloppy code) and indexed the .bam file with Pysam. Currently, pinaplpy does not find any successful reads, however the bam files do look ok
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The reason that pinaplpy does not find any successful reads is because it prioritises the .sam files over .bam files.
I've changed the code a bit to fix the issue temporarily (very sloppy code) and indexed the .bam file with Pysam.
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).