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cd mkdir smrnaseq_cl cd smrnaseq_cl export NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.3.1 |
Line 1: Move to your home directory.
Line 2: Make a temporary folder called smrnaseq_cl for Nextflow to test the smrnaseq pipeline.
Line 3: Change directory to the newly created folder smrnaseq_cl.
Line 4: In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this.
Line 5: Download and run the test code.
This will download the smrnaseq pipeline and then run the test code. It should take ~20-30 minutes to run to completion.
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If you are having trouble running the nf-core/smrnaseq rnaseq pipeline, some pre-computed results are provided under the folder /work/training/nextflow_intro/rnaseq_pbs.
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