-
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
…
-
BWA Mem (scattered by read group)
## Current setup:
Picard SamToFastq | BWA | Picard MergeBamAlignment
## Proposed setup:
Samtools bam2fq | BWA |
Samblaster | (mark duplicates here and remove…
-
Hi there,
I have a strange error while running operams. I launched the tool against an already computed assembly.
`OPERA-MS --short-read1 FastqIllumina/all.bbdukTrimQ15.SludgeDK_1.fastq.gz --sho…
-
I've recently suffered a lot with building an index using bwa 0.7.17 (detailed issues: https://github.com/lh3/bwa/issues/318)
So I hope to use the bwa-mem2 to make another attempt. The only questio…
-
**Three related issues:** None have been added to Roadmap for triage yet.
**BUG** Most important item to fix.
- [ ] **When workflows do not contain the optional *Inputs* dataset, and the input…
-
Rather major stuff! as discovered by @Marlies1993
`bwa mem` yields empty alignments for sequences of 25bp ...
apparently it isn't designed for 25bp, and something like `bwa aln` should be used inste…
-
I have encountered an issue where alignments have 0 MAPQ because of secondary alignments in alt contigs. This is usually fixed by bwa-postalt for regular DNA sequencing but it does not seem to work fo…
-
Hi. When running an analysis with opera-ms an error is produced:
**Error in during bwa mapping.**
I hace checked /intermediate_files/polished_assembly/bwa.err, and this is shown:
**[bam_sort…
-
Hello!
I am running bwa-mem2 2.2.1--hd03093a_5 from biocontainers using singularity. On a specific dataset (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR470/009/ERR4705259/ERR4705259_1.fastq.gz ftp://ftp.…
-
My code and printed output:
> (base) bio-24046:~ jvanderwoude3$ snippy --outdir trial --ref PAO1.gbk --R1 CF1_LeftLower_D12_R1.fastq.gz --R2 CF1_LeftLower_D12_R2.fastq.gz
> [12:13:56] This is snip…