5. Parameters

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 3.15.1.

Specifying parameters on the command line

Parameters are generally specified on the CLI (i.e. command line interface).

Example of parameter specifications for the nf-core/rnaseq pipeline

nextflow run nf-core/rnaseq -profile singularity -resume -r 3.14.1 \
        --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 "

Exercise 2

We will rerun the same smrnaseq test pipeline on the command line but adding a new parameter which specifies the name of the multiqc report to “smrnaseq_multiqc_report.html”. Important, rerun using the option -resume so it uses the cached results. We will cover this in the next section.

cd ~/smrnaseq_cl
nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 -resume --multiqc_title smrnaseq

For all steps that are not affected by the updated parameter, the pipeline does not rerun these steps but instead uses the results that have been cached.

The last MULTIQC step is the only one to be rerun.

The new smrnaseq_multiqc_report.html file can be found under the results/multiqc folder.