Entering edit mode
21 months ago
optimistsso4co3 ▴ 100
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
The fastest way to get help for nf-core pipelines is to join the Slack: https://nf-co.re/join/slack
I currently see no way to pass in a custom argument such as
--adapter, so this would need to be added by the pipeline developers.
So eventually via config file or command like you could add:
or if you specify nothing then this will be an empty string and gets ignored. Just ask at the Slack, they are helpful and friendly guys.
The bad solution i use right now is just edit main.nf
Why is that bad? If the option you need is not in there you have two ways to go: a) ask for it to be added or b) fork it and add it yourself.
It becomes less reproducible that way
Also if you do open a pull request with your changes, once merged it will benefit all users :)
Wanted to note that with the upcoming DSL2 pieline release you will be able to append additional command line flags like this to _any_ process via a config file (no need to edit any pipeline files). This will be true for all nf-core pipelines as they transition to DSL2.
DSL2 = Nextflow domain specific language 2, new syntax and for nf-core marks the start of a modular design using reusable pipeline components: https://github.com/nf-core/modules