Marianas Collapsing Second Pass CWL

mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools

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Marianas Collapsing Second Pass CWL #36

Closed rhshah closed 5 years ago

rhshah commented 5 years ago

org.mskcc.marianas.umi.duplex.DuplexUMIBamToCollapsedFastqSecondPass standard-bam-file pileup-file minMappingQuality minBaseQuality mismatches wobble minConsensusPercent reference-fasta-file first-pass.mate-position-sorted.txt

This will produce collapsed_R1_.fastq and collapsed_R2_.fastq files along with some QC files.

ionox0 commented 5 years ago

we can probably close this now 💯