NF workshop UiO

Course page: https://www.mn.uio.no/sbi/english/events/oslo-bioinformatics-workshop-week-2023/index.html

Notes

Tasks: For example one task per fastq file pair. So one process for FastQC, but several tasks for each file pair.

There is something called nf-prov - for provenance and clinical data. Might be relevant for NIPH someday…

nf-test. Testing framework for Nextflow pipelines. For unit testing.

nf-core community have a big pot of hours on GitPod available to share with us…

Fix the Nextflow version before you run a pipeline. Also fix the version of the pipeline. export NXF_VER=23.10.0

The output of a process can be the standard out:

output:
stout

The work directory:

.command.run is a wrapper file around the .command.sh script. You can for example run .command.run when you use a docker container. The mounting instructions and input files will be there.

Q: How to output a value from a process into a channel?

nextflow log

You can -resume specific runs. Not only the last one.

Channel.fromPath:

Nextflow will then actually stage files into the process and not simply the filenames as strings (if e.g., with channel.of()).

config: process.MULTIQC.container = ‘’ process withName: {

}

nf-core create-params-file

Will create a params file based on the needed parameters of the pipeline

Use branch to split the samplesheet by AGENS?

NF-core

Shared configs. For example for different clusters. Test data: https://nf-co.re/docs/contributing/test_data_guidelines
https://github.com/nf-core/test-datasets Nextflow will recognize https or ftp addresses to files and automatically download them.

Add pipeline: https://nf-co.re/docs/contributing/adding_pipelines

Automation

Harshil Patel talk in the Barcelona 2023 Summit. Automation of the Seqera platform.

Random notes

Don’t need to specify main.nf. Just give the directory name to nextflow run.

nf-core tools can also remove a module.

Can install subworkflows with nf-core tools instead of modules. E.g. bowtie align samtools…

nextflow run somepipeline –help - the help menu comes from the schema file.

How to edit the schema file:

nf-core schema build They have a web builder also.