Data Analysis Modules: panoply_quilts

panoply_quilts

Description

Workflow to perform QUILTS (https://github.com/ekawaler/pyQUILTS) on sample data (somatic, germline, splice junction, and fusion). QUILTS produces a custom protein database which can be used in mass spectrometry searches.

Input

Required inputs:

• junction_file_type: (String default = 'star') String to indicate what junction finding software was used (only accepts star, MapSplice, or tophat).
• out_file: (String default = 'quilts_results.tar.gz') Name of the output file produced.
• output_dir: (String default = '/src/QUILTS/output') Where the QUILTS data will be deposited on the docker.
• reference_genome: (File default = 'gs://fc-5a1bdedd-17aa-4a16-b661-bc16902fc4e0/genome/emily_ensembl_hg38.tar.gz') A compressed file containing the genome to be used by QUILTS. See the pyQUILTS repository for more info on making a genome for QUILTS use. By default an ensembl hg38 genome is used. More premade genomes are available on the Terra workspace 'QUILTS_data' google bucket.
• reference_proteome: (File default = 'gs://fc-5a1bdedd-17aa-4a16-b661-bc16902fc4e0/proteome/emily_ensembl_v100_hg38.tar.gz') A compressed file containing the proteome to be used by QUILTS. See the pyQUILTS repository for more info on making a proteome for QUILTS use. By default an ensembl version 100 hg38 proteome is used. More premade proteomes are available on the Terra workspace 'QUILTS_data' google bucket.
• At least one of:
• input_somatic_vcfs: (array of .vcf files) Somatic files must be in .vcf format. This input can take an array of files but only input arrays of files if you wish for the output to be a merged file containing all results. If you wish to run QUILTS on a per sample basis please enter only one data file in these input array fields.
• input_germline_vcfs: (array of .vcf files) Germline files must be in .vcf format. This input can take an array of files but only input arrays of files if you wish for the output to be a merged file containing all results. If you wish to run QUILTS on a per sample basis please enter only one data file in these input array fields.
• input_gene_fusions_files: (array of .txt files) Gene fusions files must be a .txt in the following format:

FusionName LeftBreakpoint RightBreakpoint Sample JunctionReadCount GENE1—GENE2 chr19:1000000:- chr16:500003:+ Sample1 5

This input can take an array of files but only input arrays of files if you wish for the output to be a merged file containing all results. If you wish to run QUILTS on a per sample basis please enter only one data file in these input array fields.

• input_splice_junctions_files: (array of either .txt, .tab, or .bed files) Splice junction files must be either .txt for MapSplice results, .tab for STAR results, or .bed for tophat results. This input can take an array of files but only input arrays of files if you wish for the output to be a merged file containing all results. If you wish to run QUILTS on a per sample basis please enter only one data file in these input array fields.

Optional inputs:

• threshB: (integer) Please see the pyQUILTS repository for more information on this input.
• threshD: (integer) Please see the pyQUILTS repository for more information on this input.
• threshN: (integer) Please see the pyQUILTS repository for more information on this input.
• variant_quality_threshold: (integer) Please see the pyQUILTS repository for more information on this input.

Output

• outputs: (File .tar.gz) The name of this output depends on the input to out_file above. This file contains the results of the QUILTS run in a compressed format.