Ideas for adding metadata handling to Genomics

hello-channels

An additional module that would fit between hello-gatk and hello-modules.

Aims:

• Teach users about the concepts of channels and functional programming with Nextflow
• Teach users about data structure within channels
• Teach users practical examples of operators to manipulate channels

Proposal:

Subject to change, this part might need further discussion.

From the hello-gatk pipeline, add the following features stepwise

1. Use a samplesheet to read in the BAM files (splitCsv)
2. Add a sample ID to each BAM file (tuples)
3. Pass the tuple between all processes with a manipulation (map)
4. Group per family ID (groupTuple)
5. Create samplesheet output

Key targets:

• view for debugging
• map for manipulating channel contents
• 1 to 3 more advanced operators such as collectFile, groupTuple, join for demonstrating how channels can be manipulated with built in methods.

To do:

• Write final endpoint pipeline to be aiming for
• Write intermediate steps as tutorial
• Add any changes to hello-modules and hello-nf-test that need to be included

Related issues

https://github.com/nextflow-io/training/issues/361
https://github.com/nextflow-io/training/issues/359