pecgs-fusion

cwl wrapper for dinglab fusion pipeline

based on dinglab fusion pipeline

Running pecgs fusion on compute1

notebook for generating test run

notebook for generating cwl test run on compute1

directory with scripts to run test sample on compute1

Running fusion.py

Arguments

usage: fusion.py [-h] [--cpu CPU] [--genome-lib-dir GENOME_LIB_DIR] [--genome-db GENOME_DB] [--bwts BWTS] [--filter-database FILTER_DATABASE] [--fusion-annotator-dir FUSION_ANNOTATOR_DIR] [--integrate-executable INTEGRATE_EXECUTABLE] [--integrate-fasta INTEGRATE_FASTA] [--integrate-annotations INTEGRATE_ANNOTATIONS] [--combine-call-script COMBINE_CALL_SCRIPT] [--filter-script FILTER_SCRIPT] sample fq_1 fq_2

positional arguments:

• sample
  • Sample id
• fq_1
  • RNA-seq fastq 1
• fq_2
  • RNA-seq fastq 2

optional arguments:

• -h, --help

  • show this help message and exit

• --cpu CPU

  • Number of CPUs to run on

• --genome-lib-dir GENOME_LIB_DIR

  • GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir directory location

• --genome-db GENOME_DB

  • ericscript_db_homosapiens_ensembl84 directory location

• --bwts BWTS

  • bwts location

• --integrate-fasta INTEGRATE_FASTA

  • fasta used during integration step

• --filter-database FILTER_DATABASE

  • Filter database location. ....../FilterDatabase

• --fusion-annotator-dir FUSION_ANNOTATOR_DIR

  • fusion annotation location. ....../FusionAnnotater

• --integrate-executable INTEGRATE_EXECUTABLE

  • Location of Integrate executable

• --integrate-annotations INTEGRATE_ANNOTATIONS

  • location of annot.ensembl.GRCh38.txt used during integration step

• --combine-call-script COMBINE_CALL_SCRIPT

  • location of combine_call.pl

• --filter-script FILTER_SCRIPT

  • location of filter.pl

Docker

docker image is available from dockerhub (estorrs/pecgs_fusion:0.0.2)