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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 " |
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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 ~$HOME/workshop/2024-2/session3/smrnaseq_cl nextflow run nf-corefile:///work/training/smrnaseq -profile test,singularity --outdir results -r 2.3.1 -resume --multiqc_title smrnaseq |
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