Pipeline parameters

The pipeline currently uses the following parameters.

name	meaning	default
--outdir	output directory	results
--catalog_file	sample catalog file	s3://zhanglab-pancancer/assets/CPTAC3.Catalog.dat
--genome_basedir	location that contains genome index and annotation files	s3://zhanglab-pancancer/reference/GRCh38.p13
--genome_ref_prefix	prefix for genome reference file	GRCh38.p13.genome.fa
--genome_ref	path to the genome reference file	s3://zhanglab-pancancer/reference/GRCh38.p13/GRCh38.p13.genome.fa
--genome_ref_index	path to the genome index files	s3://zhanglab-pancancer/reference/GRCh38.p13/GRCh38.p13.genome.fa.*
--genome_ref_anno	path to genome annotation file	s3://zhanglab-pancancer/reference/GRCh38.p13/gencode.v34.basic.annotation.flat.gtf
--data_source	location type of the fastq files (gdc,s3 or local)	gdc
--run_indexing	whether or not to index the reference genome	false
--start, --end	starting/ending index for the samples need to be processed	-1 for both, which means all samples in the case id file (source type: gdc) or all samples in the catalog file (source type: local or s3)
--allow_dup	whether or not to allow duplicated sample names in the catalog file, applies to gdc case only	false
--gdc-token	path to GDC token file for downloading data from GDC