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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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In the screenshot below, all the jobs which will be run are listed.
We can see that 3 7 jobs have started:
FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW: 3 jobs are running, the latest job that started is for sample Clone9_N1
FASTQ_FASTQC_UMITOOLS_FASTP:FASTP: 3 jobs are running, the latest job that started is for sample Clone9_N1
INDEX_GENOME (genome.fa): 1 job has started
At the bottom you can see that 6 files (including test fastq.gz input files and reference files) have also been downloaded.
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You can check the full list of jobs that have been submitted at any point in time by opening a separate terminal and using the command:
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At the bottom, the message ‘Pipeline completed successfully’ will be printed along with the duration, the CPU hours and numbers of jobs that run to completion.
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You will see that Nextflow created 2 folders (results and work) if you run the command
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ls |
You can inspect the results which have been output by typing:
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You can browse a couple of results folders to check what sort of outputs were generated by the pipeline.
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