How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well.
Here is an example of trim_galore line i want to adapt to sarek pipeline:
trim_galore
--adapter AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA
--adapter2 AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG
--quality 20
--paired
--no_report_file
reads1.fq.gz
reads2.fq.gz
And here is an example of sarek comman line i would like to pass these trim_galore parameters to:
nextflow run nf-core/sarek
--input samples.tsv
--split_fastq 2000000
--tools 'HaploTypeCaller'
--genome GRCh38
--save_reference
--species 'homo_sapiens'
-profile singularity
--trim_fastq
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