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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