Duke-GCB/bespin-cwl

Issues

• Archive repository

  #80 opened 5 years ago
  0

• gatk4 exomseq error in joint-genotyping

  #78 opened 5 years ago
  2

• exome-seq: allow variant recalibration to fail

  #73 opened 6 years ago
  0

• Replace python helper scripts with bespin-cli calls

  #69 opened 6 years ago
  0

• Specify file formats

  #66 opened 6 years ago
  0

• Clarify the workflows section in CircleCI config

  #64 opened 6 years ago
  0

• Restructure packed workflows and versioning

  #62 opened 6 years ago
  3

• exome-seq: step/tool to concatenate multiple FASTQ files

  #59 opened 6 years ago
  1

• exome-seq: FastQC memory requirements are too low when threads are high

  #56 opened 6 years ago
  2

• trim_galore: outputs no trimmed files when paired=false

  #49 opened 7 years ago
  0

• exomeseq: Add choice input for "Small Familial" or "Large Population" study

  #48 opened 7 years ago
  0

• Generate packed workflows using CI and upload as GitHub release

  #44 opened 7 years ago
  1

• exome-seq: default InbreedingCoeff annotation causes failures

  #43 opened 7 years ago
  1

• exome-seq: input paired reads as named pairs of files

  #40 opened 7 years ago
  0

• exome-seq: HaplotypeCaller cannot emit a BAM file in multi-threaded mode.

  #38 opened 7 years ago
  1

• exomeseq-methods: use author year reference indicators

  #36 opened 7 years ago
  2

• exome-seq: include checksums and source url for bespin sample input files

  #35 opened 7 years ago
  0

• exomeseq-methods: File naming and formatting

  #33 opened 7 years ago
  0

• exome-seq: Include SoftwareRequirements

  #31 opened 7 years ago
  0

• exome-seq: Correct output type for hs_metrics_dir

  #29 opened 7 years ago
  1

• exome-seq: Optimize BedToIntervalList steps

  #28 opened 7 years ago
  0

• exome-seq: Look into custom data type for Pair of FASTQ Files

  #25 opened 7 years ago
  1

• exome-seq: support for merging/concatenating input reads

  #24 opened 6 years ago
  2

• Packed exome seq workflow fails validation

  #22 opened 7 years ago
  1

• exome-seq: results output organization and file changes

  #20 opened 7 years ago
  4

• exome-seq: Fix indels/SNP calling

  #19 opened 7 years ago
  0

• exome-seq: break workflow into steps

  #17 opened 7 years ago
  0

• exome-seq: Implement QC reports step

  #16 opened 7 years ago
  2

• exome-seq: Improve file naming conventions for part 2

  #15 opened 7 years ago
  2

• exome-seq: GATK-HaplotypeCaller fails in libVectorLoglessPairHMM

  #14 opened 7 years ago
  1

• exome-seq: Include capture kit parameters

  #13 opened 7 years ago
  1

• exome-seq: extract read group information

  #12 opened 7 years ago
  1

• exome seq - update docker images and pin to tags

  #9 opened 7 years ago
  2

• exome seq: Missing secondary files when running with cwltoil

  #8 opened 7 years ago
  1

• exome seq: missing index after picard-MarkDuplicates

  #7 opened 7 years ago
  2

• exome seq: Error parsing SAM header

  #6 opened 7 years ago
  4

• Provide additional samples for joint genotyping

  #5 opened 7 years ago
  0

• Packed workflows not readable in latest cwltool

  #3 opened 7 years ago
  0

• Add License

  #1 opened 8 years ago
  1