Installation

See this.

How to run

Prepocessing

Output filename will be suffixed with .trimmed and outputs will be stored on gs://input-data-mirrored/input_fastqs/trimmed.

$ preprocess/trimmomatic_gs.sh [FASTQ_GS_URI] [BASENAME_OF_TRIMMED_FASTQ]

Processing

Find a template JSON process/sample.json

$ caper submit process/chip.ihec.docker.wdl -i INPUT_JSON

Check workflow's status. You can also get WORKFLOW_ID, which will be used for post-processing.

$ caper list

Postprocessing

Based on this code

Deidentify experiment BAMs and control BAMS. Then make a bamCoverage signal track for experiment BAMs. This script will find all BAMs on WORKFLOW_ROOT_GS_URI and store postprocessed outputs on OUTPUT_DIR_GS_URI. NO TRAILING SLASH ALLOWED FOR GS URI!

$ cd postprocess # will make tmp directory inside it
$ ./postprocess_gs.sh [WORKFLOW_ROOT_GS_URI] [OUTPUT_DIR_GS_URI]