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Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test
### Is your feature request related to a problem? Please describe
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I had to add --no-PG to my ubam generation code to avoid name collisions.
to reproduce create a ubam with samtools cat and samtool collate.
then use samtools collate to product the aligned bam.
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Replace the GATK steps with samtools pileup so it removes the GATK dependency.
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I managed to get samtools 1.2 support added in a `samtools-1.2-cjf` branch (this is based off the `samtools-1.1` branch by @lstein ).
A few clunky things probably need to be cleaned up:
1. The libr…
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Hello, thanks for the plugin!
I am having some issues with it, though. It is apparently deleting intermediate files marked for use in upcoming processes. When running my pipeline (which I created m…
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![2ndAttempt MergeAllReads monitor log](https://git…
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I am attempting to run HLA-LA.pl and I get "I need samtools >=1.3" error. However, I have samtools 1.16.1 installed and it is in the correct identified path above this error.
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#335
I found the code you provided:
`dicey chop sacCer3.fa`
`bwa index sacCer3.fa`
`bwa mem sacCer3.fa read1.fq.gz read2.fq.gz | samtools sort -@ 8 -o srt.bam`
`samtools index srt.bam`
`dic…
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Hi,
I ran velocyto verison 0.17 with samtools version 1.15.1 with 128GB memory. My bam files were standard 10X output (STAR aligner) and they are sorted by coordinate. Why do I still get this error…
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Hi,
samtools (Version: 1.3.1 using htslib 1.3.1) reheader is changing the sequence names of some alignments.
For instance,
> samtools view torehead.bam
> SRR798041.25511018 16 V 174…