grendon

Revisiting input to Diamond when it is Paired reads.

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Hi, Do you recommend merging the paired reads with a tool like PEAR before running Diamond?

[BUG] Sentieon_BQSR is not skipped when dbsnp and indel files are not provided

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## Check Documentation I have checked the following places for your error: - [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [ ] [nf-core/sarek pipeline documentation](https://nf-co.re/sarek/usage) ## Description of the bug I...

Is the orientation parameter necessary when running metaviral with illumina PE RNASeq datasets?

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### Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above. The input is RNASeq Illumina PE. Read1 aligns...

ERROR picard container for NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS -> setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory

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### Description of the bug I am running release 2.6.0 of the viralrecon pipeline. It aborts when it gets to this step NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS. It looks like the problem is with...

What is the meaning of the third column of the output file? I just analyzed some ecoli strains that I assembled with Spades. The third column has values like 10...

Dorado duplex stand alone v 0.6.0 : when the models are in a different location. How to configure dorado to look for models elsewhere?

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# Issue Report My stand alone installation of dorado on a unix-based cluster did not come with the models. I downloaded the models manually; but dorado doesn't seem to see...

epic 0.2.9 compute_score_threshold.py:24 RuntimeWarning: divide by zero encountered in log

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I converted my BAM files to BED format with bamtobed as suggested in the tutorial. Then I run the epic command like this: > epic --treatment Amy_C2_763_C1_IP.bed \ > --control...

extract question: How to extract the unclassified reads

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Hi, The metabuli report has taxid=0 for the unclassified category. But when I try that value in the extract command to get the unclassified reads, it doesn't work. Is there...

Downsampling support

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Hi, The size of the illumina short-reads files continue to grow as the sequencing costs continue to fall. Running FastQC on the entire input file is compute-intensive. Performing the downsampling...