icgc-argo-workflows/dna-seq-processing-tools

Issues

• Improve tool `seq-data-to-lane-bam` to output ubam with required metadata in header

  #121 opened a year ago by lindaxiang
  3

• Change `tempdir` from `Path` to `Val` inputs of tools: `bwa-mem-aligner` and `bam-merge-sort-markdup`

  #122 opened 3 years ago by lindaxiang
  7

• Compress bam output

  #115 opened 2 years ago by lindaxiang
  1

• seq-data-to-lane-bam: support the situation where read_group_id_in_bam could be the same in different input BAMs

  #111 opened 4 years ago by junjun-zhang
  1

• bwa-mem-aligner: update how to find corresponding read group in metadata from input lane bam

  #110 opened 4 years ago by junjun-zhang
  1

• seq-data-to-lane-bam failed to skip all input bams when process multiple input bams

  #107 opened 4 years ago by lindaxiang
  1

• seq-data-to-lane-bam needs to avoid lane bam file collision when process multiple input BAMs

  #105 opened 4 years ago by junjun-zhang
  1

• Feature Request - add seqs_per_slice=1000 when convert to cram

  #91 opened 5 years ago by lindaxiang
  0

• 🐛 bwa-mem-aligner, change library_strategy to experimental_strategy

  #100 opened 5 years ago by junjun-zhang
  1

• Set optional output in nextflow DSL2

  #83 opened 5 years ago by lindaxiang
  1

• support user specified tmpfile path (-T) in samtools sort

  #97 opened 5 years ago by junjun-zhang
  1

• support user specified tmpfile path in bammarkduplicates2

  #96 opened 5 years ago by junjun-zhang
  1

• add parameters to config JVM options when using Picard tools

  #76 opened 5 years ago by lindaxiang
  1

• Improvement: remove crai creation step in bam-merge-sort-markdup

  #84 opened 5 years ago by junjun-zhang
  1

• Exclude secondary and supplementary alignments before convert BAM back to Fastq🐛

  #77 opened 5 years ago by lindaxiang
  1

• Use original base quality score🐛

  #78 opened 5 years ago by lindaxiang
  1

• Hashbang headers

  #71 opened 5 years ago by ewels
  2

• Fix the issues caused by repository migration🐛

  #27 opened 5 years ago by lindaxiang
  1

• Fixes to JTracker dna_seq_alignment workflow

  #25 opened 5 years ago by junjun-zhang
  1

• cwltool_launcher as Jtracker adapter to run cwl workflows and tools

  #23 opened 5 years ago by lindaxiang
  1

• prepare test datasets and tiny reference genome to test all existing tools

  #18 opened 5 years ago by lindaxiang
  1

• implement the pytest and hook it up with travis

  #19 opened 5 years ago by lindaxiang
  1

• Alignment optimization

  #11 opened 5 years ago by lindaxiang
  1

• bwa-input-prepare optimization

  #10 opened 5 years ago by lindaxiang
  1

• Add -Y -K 100000000 params to bwa mem command

  #8 opened 5 years ago by junjun-zhang
  1

• Add another markdup tool: samblaster

  #9 opened 6 years ago by junjun-zhang
  1