ENCODE Software
All software used or developed by the ENCODE Consortium
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- Croo — sourceCroo is a Python package for organizing outputs from Cromwell. Croo parses metadata.json which is an output from Cromwell and makes an organized directory with a copy (or a soft link) of each output file as described in an output definition JSON file specified by --out-def-json.Software type: framework
- Caper — sourceCaper (Cromwell Assisted Pipeline ExecutoR) is a wrapper Python package for Cromwell. Caper is based on Unix and cloud platform CLIs (curl, gsutil and aws) and provides easier way of running Cromwell server/run modes by automatically composing necessary input files for Cromwell. Also, Caper supports easy automatic file transfer between local/cloud storages (local path, s3://, gs:// and http(s)://). You can use these URIs in input JSON file or for a WDL file itself.Software type: framework
- Check Files — sourceFiles are checked to see if the MD5 sum (both for gzipped and ungzipped) is identical to the submitted metadata, as well as run through the validateFiles program from Jim Kent's source utilities.
- FASTQ read-name correctionA script resolving FASTQ read-name inconsistencies