Jim comments

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Jim

Add Singularity arguments for specific rules in Snakefile

Work on being able to use singularities with CUDA would be greatly appreciated.

Actually, I seemed to just have solved it. I think nextflow is ignoring config parameters in case these are formatted incorrectly. Try quoting your strings ``` process { withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR'...

Custom config being ignored

Actually, you probably also have to separate the properties of the two processes. ``` process { withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR' { // single job memory = '80.GB' cpus = 32 time =...

agat_sp_extract_sequences.pl does not incorporate CDS feature ID in headers

I'm not entirely sure what exactly CDS chunks refers to. Are you referring to chunks as existent on different exons?

agat_sp_extract_sequences.pl does not incorporate CDS feature ID in headers

Ok. I'm not familiar enough with annotation formats and conventions to know what the best approach is in case it's important to list what chunks a CDS is constructed from....

Question about obtaining Fastq from modification-aware dorado runs

Hi @malton-ont, Can you comment on the differing results of the FASTQ files as listed in the second issue observed: - Converting that BAM with samtools fastq gives FASTQ in...

Filtering out significantly DMR sites from `modkit dmr` output.

Would be interested in this too. Thanks