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nextflow run nf-core/rnaseq -profile test,singularity --outdir results -r 3.10.1

Running the pipeline using custom data

Example of a typical command to run an RNA-seq analysis for mouse samples:

nextflow run nf-core/rnaseq --input samplesheet.csv \
        --outdir results \
        -r 3.10.1 \
        --genome GRCh38 \
        -profile singularity \
        --aligner star_rsem \
        --clip_r1 10 \
        --clip_r2 10 \
        --three_prime_clip_r1 2 \
        --three_prime_clip_r2 2

Note, if the running was interrupted or you did not complete a particular step, or you want to modify a parameter for a particular step, instead of re-running all processes again, nextflow enables you to “-resume” the workflow.

nextflow run nf-core/rnaseq --input samplesheet.csv \
        --outdir results \
        -r 3.10.1 \
        --genome GRCh38 \
        -profile singularity \
        --aligner star_rsem \
        --clip_r1 10 \
        --clip_r2 10 \
        --three_prime_clip_r1 2 \
        --three_prime_clip_r2 2 \
      -resume

Preparing a ‘samplesheet.csv’ file

Prepare a sample sheet file that specifies the input files to be used. To do this, we use an nf-core script to generate the ‘samplesheet.csv’ file as follows:

#load python 3.7
module load phyton3.7

#download script and make executable
wget -L https://raw.githubusercontent.com/nf-core/rnaseq/master/bin/fastq_dir_to_samplesheet.py
chmod +x fastq_dir_to_samplesheet.py

#generate the samplesheet.csv file
fastq_dir_to_samplesheet.py /path/to/directory/containing/fastq_files/ samplesheet.csv \
    --strandedness unstranded \
    --read1_extension R1.fastq.gz \
    --read2_extension R2.fastq.gz

...

#delete the existing assests associated with the RNAseq pipeline:
cd ~/.nextflow/assets/nf-core
rm -r rnaseq/

#run again a test with the new version that you are testing, for example, version 3.10.1. See details on how to run a test above (under 'Getting Started')

Running the pipeline using custom data

Example of a typical command to run an RNA-seq analysis for mouse samples:

nextflow run nf-core/rnaseq --input samplesheet.csv \
        --outdir results \
        -r 3.10.1 \
        --genome GRCh38 \
        -profile singularity \
        --aligner star_rsem \
        --clip_r1 10 \
        --clip_r2 10 \
        --three_prime_clip_r1 2 \
        --three_prime_clip_r2 2

Note, if the running was interrupted or you did not complete a particular step, or you want to modify a parameter for a particular step, instead of re-running all processes again, nextflow enables you to “-resume” the workflow.

nextflow run nf-core/rnaseq --input samplesheet.csv \
        --outdir results \
        -r 3.10.1 \
        --genome GRCh38 \
        -profile singularity \
        --aligner star_rsem \
        --clip_r1 10 \
        --clip_r2 10 \
        --three_prime_clip_r1 2 \
        --three_prime_clip_r2 2 \
      -resume