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Parameters are generally specified on the CLI (i.e. command line interface).
Example of parameter specifications for the nf-core/rnaseq pipeline
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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 " |
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.
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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.
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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.