SCXA pipelines update/upgrade

[pmb59]

After few years of successful run, some upgrades can be done for workflow modernisation:

In order of priority:

• 1. Bring tertiary analysis to Nextflow, for a unified workflow
  1.1 New repo: scxa-tertiary-workflow
  1.2 adding w_tertiary to scxa-workflows repo
  1.3 Modify scxa-control-wf logic and scripts
  1.4 Edit run_tertiary_workflow.sh in scxa-workflows

• 2. Moving to DSL2 (DSL1 not working on Nextflow versions >= 22.12.0)

  2.1 Remove dependencies to channel anaconda
  2.2 Migrate main.nf

• 3. Integration with with Seqera Platform (Nextflow tower):

  3.1 to track, monitor and get detailed information regarding the execution of the pipelines
  3.2 to generate reports

• 4. Tool update, update to best practices.

Notes:

• Updating documentation, e.g. in scxa-workflows

• Review and consider incorporating nf-core standards (see guidelines and tutorials on how to contribute)

[pmb59]

Point 1 being addressed here