WIP:POC: Repo to show that we can switch from using perl modules over to using cwl modules instead.

Instructions After cloning this repository, users should first install all requirements by installing Pipenv on their machine. Please reference the Makefile.

1. make

2. make activate

Update test_data_files submodule cd tests/data git fetch git pull

To do:

• Make initial cwl tools
• cutadapt
• fastp
• bwa
• samtools
• abra
• combine intial tools into a bam generation workflow
• run locally with test data
• run on lsf cluster with test data
• Gather test_data
• T/N from CLIN 20200040 (case has mutations, copy number, fusion and CH).
• include a second pair and controls (NTC, PoolNormal, PoolTumor, BloodPoolNormal)
• make downsampled versions of the fastqs for testing locally

User Requirements: FASTQS -> bams Use CWL/DSL Use toil Test on LSF Use singularity Project structure

Tools

Merge/Trim CUTADAPT fastqc bamqc Bam Generation SAMTOOLS ABRA BWA - mem, etc... GATK - BQSR ( think about it )

There are two ideas that are starting to form here.

1. Pluggable modules a. Community Modules + MSKCC ClinBx in-house modules b. Separate ability for development and testing
2. Cookie-cutter pattern a. Separate pipeline development b. Separate pipeline requirements