czbiohub-sf/sc2-illumina-pipeline

Issues

• coverage plot per pool

  #86 opened 3 years ago by aspitaleri
  0

• duplicate in bam

  #85 opened 3 years ago by aspitaleri
  2

• trimReads fails: no file sample1_artic_R_covid_1_val_1.fq.gz

  #84 opened 3 years ago by stephlo76
  0

• Kraken DB not available any more

  #83 opened 3 years ago by stephlo76
  0

• Test fails: file missing

  #82 opened 3 years ago by stephlo76
  0

• vcf is misisng most INDELs

  #80 opened 3 years ago by danrlu
  1

• [minor] Better handling of skipping ERCC process

  #71 opened 4 years ago by jackkamm
  2

• exit and print error if kraken2_db not set

  #46 opened 4 years ago by samlhao
  2

• Allow running plain metagenomics (without MSSPE primers)

  #75 opened 4 years ago by jackkamm
  1

• [meta] Pipeline and repo cleanup

  #72 opened 4 years ago by jackkamm
  1

• Fix indel calling

  #56 opened 4 years ago by samlhao
  1

• add intrahost nucleotide diversity stat

  #55 opened 4 years ago by samlhao
  0

• add filtered_reads column to combined.stats.tsv

  #54 opened 4 years ago by samlhao
  0

• Single end fastqs

  #52 opened 4 years ago by jackkamm
  1

• Unpaired reads and bad test sample

  #51 opened 4 years ago by jackkamm
  1

• Speed up filtering step

  #50 opened 4 years ago by samlhao
  6

• visualization of read support for variants

  #45 opened 4 years ago by samlhao
  0

• Add annotation step with VADR

  #43 opened 4 years ago by jackkamm
  0

• Automated reporting of newly assembled genomes

  #38 opened 4 years ago by batson
  0

• use pangolin for lineage assignment

  #18 opened 4 years ago by samlhao
  1

• Add License

  #78 opened 4 years ago by batson
  3

• Unit tests for ARTIC

  #70 opened 4 years ago by jackkamm
  1

• Avoid +N insertions

  #73 opened 4 years ago by jackkamm
  0

• Error running pipeline when sample size is 2 or less

  #68 opened 4 years ago by nhatas
  5

• skip trimming primers

  #67 opened 4 years ago by nhatas
  1

• Fix/remove test_fasta_reads, test_single_end

  #65 opened 4 years ago by jackkamm
  0

• exit with error message if reads not found

  #63 opened 4 years ago by samlhao
  0

• Document everything

  #28 opened 4 years ago by samlhao
  1

• Rename this repo

  #41 opened 4 years ago by jackkamm
  1

• Test data configs are not portable

  #47 opened 4 years ago by evanfloden
  0

• Improved VCF files

  #40 opened 4 years ago by jackkamm
  0

• Prefilter human reads as first step in pipeline

  #31 opened 4 years ago by jackkamm
  0

• call_consensus test fails: missing parameter `reads`

  #35 opened 4 years ago by batson
  2

• implement masking

  #32 opened 4 years ago by samlhao
  0

• Retain top BLAST hit from multiple geographic regions

  #23 opened 4 years ago by batson
  0

• New mutations is an overestimate

  #13 opened 4 years ago by jackkamm
  4

• Add trim-galore back to multiqc

  #10 opened 4 years ago by jackkamm
  0