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Hello,
Thank you for your software! After running MitoHifI I am receiving an error that suggests that there are two entries in the all_potential_contigs.fa file. I looked at them using `grep` and t…
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### Description of the bug
Hey!
I was running the nascent pipeline v2.1.1 (v2.2.0 didn't work due to #) for two runs of the same sample.
I encountered an error at the step of `samtools sort`:
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gridss conda installation
jar file 2.13.2-gridss-jar-with-dependencies.jar
platform : Ubuntu 22
The code I ran
`gridss -t 20 -r ./reference/Ref/GRCh38.p14.genome.fa -j ~/tools/gridss-2.13.2-gri…
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Issue by @meixilin, moved here from https://github.com/moiexpositoalonsolab/grenepipe/issues/36#issuecomment-2270384816
Hi,
I have an issue that might be relevant to this thread. I have noticed…
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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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### Description of feature
With the new template sort Samtools markdup is supposedly much faster than GATK Markduplicates while having similar results.
I think this would be worth to add a faster…
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### Description of bug
Hi @ewels
Given this tree structure, I am trying to run multiqc
- there are 6 files each for stats, idxstats, flagstat
![image](https://user-images.githubusercontent.c…
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### Description of the bug
Hi,
I have been using nf-core/rnasq for a long time, but with the update of Nextflow, I am receiving the following error messages. I downloaded my fastq files with asper…
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Hi,
I got an error with samtools 1.18-7-gae19296 using htslib 1.18-17-g5acbc15, both on mac and centos7
I used the exact commands on Centos
On MAC I got a samtools config error (ld: unknown optio…
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Meta issue from #6628 for more discussion and dropping some resources.
We might need to do some benchmarking of the biggest bottleneck modules.