CAW

Nextflow Cancer Analysis Workflow Prototype developed at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.

Version

0.9.9

Authors

Sebastian DiLorenzo (@Sebastian-D)
Jesper Eisfeldt (@J35P312)
Maxime Garcia (@MaxUlysse)
Szilveszter Juhos (@szilvajuhos)
Max Käller (@gulfshores)
Malin Larsson (@malinlarsson)
Björn Nystedt (@bjornnystedt)
Pall Olason (@pallolason)
Pelin Sahlén (@pelinakan)

Installation and first execution

To use this pipeline, you need to have a working version of Nextflow installed.

See the Install Nextflow documentation
See the first execution documentation

Usage

See the usage documentation

Workflow processes

See the processes documentation

TSV files

See the workflow TSV file documentation

Use cases

See the workflow use cases documentation

Tools and dependencies

nextflow >= 0.22.1
bwa 0.7.8
samtools 1.3
picard 1.118
GATK 3.6
R 3.2.3
gcc 4.9.2
perl 5.18.4
strelka 1.0.15
manta 1.0.0
MultiQC 0.9
FastQC 0.11.5