Add BAM Umend QC as an option

[jvivian]

• Input
  • STAR BAM
• Output
  • readDist.txt: The output of RSeqQC read_distribution.py (~1kb)
  • bam_umend_qc.tsv: uniqMappedNonDupeReadCount, estExonicUniqMappedNonDupeReadCount and PASS/FAIL
  • bam_umend_qc.json: Same as bam_umend_qc.tsv but in json format
  • sortedByCoord.md.bam: BAM with duplicates marked sorted by coordinate
  • sortedByCoord.md.bam.bai: Index for sortedByCoord.md.bam
• Command
  • docker run --rm \ -v :/inputs/sample.bam \ -v :/outputs \ -v :/tmp \ ucsctreehouse/bam-umend-qc \ /inputs/sample.bam \ /outputs

https://github.com/UCSC-Treehouse/bam-umend-qc

[jvivian]

• [x] Add tool to quay.io/ucsc_cgl
• [x] Adjust config
• [x] Modify wrapper options for docker version
• [x] Write job function
• [ ] Test