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Finding list of parameters available
For the nf-core pipelines, the tools implemented and the range of parameters available are generally described in the Usage section. Some of the parameters will be required, others optional.
Let’s have a look at the nf-core/rnaseq pipeline:
All the parameters available will also be listed under the Parameters section:
Exercise 1
Using the usage and parameters sections, search how many aligner options are available for the nf-core rnaseq pipeline version 3.14.0 .
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There are 3 aligner algorithms available: 'star_salmon', 'star_rsem' and 'hisat2'. |
Specifying parameters on the command line
Parameters are generally specified on the CLI (i.e. command line interface).
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nextflow run nf-core/rnaseq -profile singularity -resume \
--input samplesheet.csv \
--outdir results \
--genome GRCm38 \
--aligner star_salmon \
--extra_trimgalore_args "--quality 30 --clip_r1 10 --clip_r2 10 --three_prime_clip_r1 1 --three_prime_clip_r2 1 " |