Skip to content

Oncogenomics_NF_WF 5.3.0

Choose a tag to compare

View all tags
@vinegang vinegang released this 24 Mar 13:47
5.3.0
73af2ac
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

🚀New Features

  • Workflow Enhancements for Capture Kit seqcapez.hu.ex.utr.v1 - Integrate the new design and target files into the pipeline.
  • Improve support for Normal-Exome and Tumor-RNAseq combinations in the DBinput_exome_rnaseq process.
  • Tumor-RNAseq workflow now account for cases where a normal exome is paired only with tumor RNA-seq.
  • Add aws_params and workflow-specific parameter files for AWS processing.
  • Add inputs for all workflows to support flexible execution in cloud environments.
  • Integrate logic to handle Xeno_DNA and Xeno_RNA data types within workflows.
  • Refactor main.nf for more streamlined workflow initiation.
  • Update launch.sh to incorporate logic from nf.sh, simplifying execution on biowulf.

🛠 Fixes

  • Avoid workflow triggers by replacing reduce operator functions (Tumor-RNAseq-specific issue).
  • Added -p flag to mkdir step to prevent run errors in Healthomics.

🔧 Refactoring & Maintenance

  • Remove FastQC from Exome_common_WF.nf as it’s now included in subworkflow-Bam_picard subworkflow.
  • Update the Prepare_samplesheet and run command processes for improved clarity and usability.
  • Remove unused resultsdir and logdir parameters from config.
  • samplesheet_builder.py output generation is now conditional on non-empty columns and valid capture kits.
Assets 2
Loading