Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph ST520110.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520110.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph FastQC - a quality control tool for high throughput sequence data

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

 https://github.com/datirium/workflows.git

Path: workflows/fastqc.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph ST520111.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520111.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph ST520115.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520115.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph ST520113.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520113.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph ST520117.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520117.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph ST520114.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520114.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph ST520105.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520105.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0
workflow graph BWA index pipeline

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

https://github.com/datirium/workflows.git

Path: workflows/bwa-index.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph ST520107.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520107.cwl

Branch/Commit ID: 0e6cfe0646173e228b2fce63e23ed8f9d78598b0