https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.5.0

🚀 Release highlights This release includes unification of AWS healthomics and biowulf pipeline versions.

✨New Features

• Unified Workflow Completion Tracking

  • Refactored creation of successful.txt to be process-based instead of Groovy script for proper pipeline completion on healthomics.
  • Introduce Allstepscomplete process to all the workflows (Exome, Tumor-Normal, RNA-seq, RNA-seq multi-lib).
  • Add a global ch_allcomplete channel to capture outputs from key processes and signal workflow completion.
  • Generate a successful.txt marker file upon completion for downstream tracking (e.g., AWS Step Functions integration).

• New Configuration Options

  • Add support for hg38 with a dedicated configuration file. - In progress
  • Update AWS-specific config (awsnextflow.config) and renamed local cluster config to biowulfnextflow.config for clarity.

• Enhanced Compatibility

  • Add a conditional check to prevent FusionCatcher failures when no fusions are detected.
  • Remove the trap command from the OptiType process to avoid HealthOmics execution errors.

🛠️ Improvements

• Output Standardization

  • Update output tuple formats across multiple processes for better compatibility.
  • Capture meta information into the output config file for easier downstream parsing.

• Docker and Tool Updates

  • Update Strelka Docker image to the latest compatible version.

- Nextflow
Published by vinegang 12 months ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.4.0

🚀 Release Highlights This release includes several new features, improvements, and bug fixes focused on enhancing CNV annotation, handling complex inputs, improving AWS integration, and better parameter parsing.

✨ New Features

• CNVKit Enhancements

  • Introduce cnvkit_annotation process and supporting Python script.
  • Add Docker image and cluster resources for cnvkit_annotation.
  • Update cnvkitpaired process to consume outputs from Mutect and Sequenza.

• Mutational Signature Logic

  • Conditionally run mutational signature analysis only when mutation count > 50.

• RNA and Sample Metadata Handling

  • Improve support for multiple RNA libraries tied to the same tumor library.
  • Enhance handling of comma-separated lists in sample inputs.
  • Extracte and pass patientID and casename to AWS utility functions.

• Mutation Burden Support

  • Add mutation burden reference for seqcapez.rms.v1 kit.
  • Integrate mutation burden calculation logic for this kit.

🛠 Improvements

• Refactor onComplete block and Groovy functions to use patientID and casename instead of nextlfow workflow parameters.(As these cannot be used on healthomics)
• Include updated publishDir logic to ensure FastQC results appear under the results/ folder.
• Remove sh from shell scripts that caused compatibility issues on AWS healthomics

🐞 Bug Fixes

• FusionCatcher - Include graceful exit when FusionCatcher returns no results, avoiding unnecessary failures.
• SampleSheet Parsing - Improve logic to robustly extract patientID and casename even with comma-separated entries.
• Add Platform as a configurable parameter.

- Nextflow
Published by vinegang about 1 year ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.3.0

🚀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 DBinputexomernaseq 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 XenoDNA and XenoRNA 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 ExomecommonWF.nf as it’s now included in subworkflow-Bampicard subworkflow. - Update the Preparesamplesheet 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.

- Nextflow
Published by vinegang over 1 year ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.2.1

New Features & Enhancements

• Update permissions for all files and folders in the work directory after workflow execution.

Bug fix

• The successful.txt file is now properly overwritten when the pipeline is re-run

Chores - Bump version number

- Nextflow
Published by vinegang over 1 year ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.2.0

New Features & Enhancements

• Expanded Tumor-RNAseq Workflow: Until version 5.1.2, the workflow supported only a single pair of Exome-RNAseq libraries per case. Version 5.2.0 now supports handling any combination of Exome-RNAseq libraries.
• New DBinput Process: Introduces a new process to generate results for the updated Tumor-RNAseq workflow.
• Enhanced split_samplesheet.py: Now supports multiple Exome and RNAseq libraries per case.

Chores

• Tag Update: Changed tag to meta.id for Combine_customRNAQC and RNAqc_TranscriptCoverage processes.
• Version Update: Bumped version number.

- Nextflow
Published by vinegang over 1 year ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.1.2

Bug Fixes:

• DBsnp reference file paths on biowulf changed causing errors. A copy of DBsnp files are made to khanlab folder and file path updated.

Chores/Misc:

• Update tsv2html.sh script to extract pipeline version from config file.
• Update Genotyping_sample process to include pipeline version as input to tsv2html.sh script.
• Update pipeline version number.

- Nextflow
Published by vinegang over 1 year ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.1.1

Bug Fixes:

• Increase maxReadsInmemory for GATK step from 500000 to 1500000 by addind --maxReadsInMemory parameter. This helps pipeline from failing due to lack of memory for deep sequences samples.

Chores/Misc:

• Update email recipients list for pipeline completion emails.
• Update pipeline version number.

- Nextflow
Published by vinegang over 1 year ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - Oncogenomics_NF_WF 5.1

New Features/Enhancements: - Add Mantis to calculate MSI for tumor-normal pairs - Add Versions.yml to include version information for every tool used in the pipeline - Add Mouse workflow to perform mapping and rsem steps for downstream analysis. - Add Optitype and HLA-HD tools for HLAcalling. - Update command line in Readdepth and Coverage process. Add sort step for bed file and include -sorted option. This will reduce high memory usage for these processes. - Update bedtools command line. From bedtools 2.22.4 command line is reversed a=bed file and b=bam file - Update `QCstats_Final.py` script python2 to 3 and add additional functionality to process hsmetrics file and extract values for mean bait coverage and mean target coverage.

Bug Fixes: - Update multipletumor and multipleRNA workflows to handle variable no. of libraries per casename. - For deep sequenced files having a gz file as input for Sequenza process is causing memory errors on biowulf. Fix this by updating the input format. - Add "PASS" filter as criteria to filter variants from strelka2 output in vcf2txt.pl script.

Chores/Misc: - Remove deprecated code file Runuptoquants.sh - Combine genotyping results and pipeline completed status emails into one email. - Add bco json and manifest json file generation for logs. - Create detailed documentation in git pages. - Remove platypus and freebayes code from vcf2txt.pl script - deprecated code. - Remove code for old HLAcalling tools(seq2HLA and HLAminer)

- Nextflow
Published by vinegang almost 2 years ago

https://github.com/ccrgeneticsbranch/oncogenomics_nf_wf - vPOC - version 5.0

POC working version. Works on: - AWS AGC - Biowulf

- Nextflow
Published by kopardev over 3 years ago