{"repo":"NCI-GDC/gdc-dnaseq-cwl","free":true,"listed":false,"github":"https://github.com/NCI-GDC/gdc-dnaseq-cwl","clone":"git clone https://github.com/NCI-GDC/gdc-dnaseq-cwl.git","description":"CWL for GDC DNASeq workflows","language":"Common Workflow Language","stars":24,"topics":["cwl","bioinformatics","workflow"],"license":"Apache-2.0","category":"workflow-automation","readme_excerpt":"GDC DNA-Seq Alignment Workflow This workflow takes a set of input WGS/WXS/Targeted Sequencing FASTQ/BAM files and generates a harmonized BAM file and an sqlite database of various metrics collected. License Note This repository is licensed under Apache License Version 2.0. Exceptions are code blocks licensed under CC-BY-SA-4.0. The CC-BY-SA-4.0 code blocks are denoted by /begin CC-BY-SA-4.0 to /end CC-BY-SA-4.0 . Environment Pre-requisites Workflow development requires the following programs installed: - docker - just - python =3.8 - cwltool==3.1.20230213100550 These workflows are developed and tested on Ubuntu. Ubuntu 20.04 The CWL is developed for cwltools version 3.1.20230213100550 https://www.commonwl.org/ GDC Users There are two entry points: - harmonization of FASTQ and BAM data: gdc-dnaseq-aln-cwl/gdc dnaseq.bamfastq align.workflow.cwl . - trusted pre-aligned data: gdc-dnaseq-prealn-cwl/gdc dnaseq.aligned reads.workflow.cwl . For external users The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in GDC reference files. For any questions related to GDC data, please contact the GDC Help Desk at support@nci-gdc.datacommons.io. The entrypoint CWL workflow for external users is subworkflows/main/gdc dnaseq main workflow.cwl . An example input yaml is available here: example/gdc dnaseq main workflow example input.yaml . Inputs Name Type Description ----","default_branch":null,"files":null,"tree":[],"storefront":"/r/NCI-GDC","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/NCI-GDC/gdc-dnaseq-cwl/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}