connor-lab/ncov2019-artic-nf

Issues

• Executions fails because Nextflow preview function is deprecated

  #134 opened 8 months ago by alethomas
  0

• A new release for this pipeline ?

  #117 opened 3 years ago by valentinelsra
  2

• SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

  #119 opened 3 years ago by thomasbtf
  0

• Pin pip version in environment.yml

  #116 opened 3 years ago by MattBashton
  0

• readgroup not found in provided primer scheme (1) for V4 scheme

  #111 opened 3 years ago by esha-joshi
  5

• articDownloadScheme isn't working with default URL

  #71 opened 3 years ago by ctr26
  7

• docker profile not working

  #95 opened 4 years ago by rrdavis77
  3

• Guppyplex step not working

  #108 opened 3 years ago by KevinMenden
  0

• Snakemake file

  #102 opened 4 years ago by ksw9
  1

• GFF included repo doesn't include ORF1ab frameshift

  #110 opened 3 years ago by tnguyensanger
  0

• New protocolo Nanopore V1200

  #105 opened 3 years ago
  0

• variants with low SupportFraction change the sequence

  #103 opened 3 years ago by paraslonic
  0

• Unparseable date error

  #104 opened 3 years ago by wtmatlock
  1

• type_vcf.py doesn't handle variants with consequence 'stop_retained'

  #90 opened 4 years ago by dfornika
  0

• Access to undefined parameter 'gff'

  #94 opened 4 years ago by hodeco
  2

• Nanopore-conda-environment.yaml update

  #97 opened 4 years ago by tarah28
  0

• Frameshift variants may interfere with typing in type_vcf.py, even with low ALT_FREQ

  #92 opened 4 years ago by dfornika
  7

• Failed samples

  #96 opened 4 years ago by gdauria
  0

• Error: prepareReferenceFiles

  #86 opened 4 years ago by yockping
  4

• Using the pipeline for non-artic primers?!

  #93 opened 4 years ago by ahmedmagds
  2

• Make QC cutoffs configurable, but with sensible defaults

  #89 opened 4 years ago by m-bull
  0

• Add --force-no-qc flag

  #88 opened 4 years ago by m-bull
  0

• Sample names inherit part of illumina's nomenclature for index and lane

  #87 opened 4 years ago by MattBashton
  0

• Update documentation

  #85 opened 4 years ago by m-bull
  0

• Add variant count for each gene to qc.csv

  #84 opened 4 years ago by m-bull
  0

• Update to ivar 1.2.4

  #80 opened 4 years ago by m-bull
  0

• Docker build is missing tools in environment.yml

  #25 opened 4 years ago by mikek498
  0

• Error: Nextflow

  #67 opened 4 years ago by yockping
  1

• Oxford Nanpore data in pipeline

  #72 opened 4 years ago by ctr26
  2

• Maintain changelog and have tags

  #17 opened 5 years ago by sb10
  2

• Command failed: nanopolish index

  #73 opened 4 years ago by sthifx
  2

• V3 bed file has incorrect format

  #28 opened 4 years ago by thanhleviet
  4

• Compilation error on Azure (Ubuntu 18.04)

  #46 opened 4 years ago by delfair
  2

• No default Qt backend for graphics when using -profile conda

  #59 opened 4 years ago by nodrogluap
  0

• ivar 1.2.3 conda dependency conflict

  #65 opened 4 years ago by jts
  1

• Nanopolish Pipeline keeps failing at `artic_plot_amplicon_depth` step

  #47 opened 4 years ago by DarianHole
  13

• Synching with fieldbioinformatics

  #38 opened 4 years ago by jts
  5

• workflow failure w/ cmd exit status 0 and 2 (w/ cmd error exit status 125)

  #42 opened 5 years ago by mjpworth
  1

• conda profile can't find extras.yml

  #40 opened 5 years ago by sb10
  0

• schemeRepoURL can no longer be used with local path

  #20 opened 5 years ago by sb10
  1

• Check for `nanoporeBarcodeDirs` doesn't work for S3 path

  #36 opened 5 years ago by lch14forever
  3

• WARN: Process 'ncovIllumina:sequenceAnalysis:writeQCSummaryCSV' cannot be executed by 'google-lifesciences' executor -- Using 'local' executor instead

  #32 opened 5 years ago by mikek498
  13

• Error running articGuppyplex

  #31 opened 5 years ago by sthifx
  2

• Error running Illumina process 'ncovIllumina:sequenceAnalysis:readMapping'

  #30 opened 5 years ago by mikek498
  2

• mandatory parameters in medaka subworkflow

  #29 opened 5 years ago by nbargues
  2

• --prefix option shouldn't be allowed to contain "/"

  #27 opened 5 years ago by m-bull
  1

• reconcile nextflow profiles

  #21 opened 5 years ago by thanhleviet
  3

• Add guppy_barcoder

  #9 opened 5 years ago by iferres
  2

• zcat step fails on OS X

  #7 opened 5 years ago by embatty
  0

• ivar command line error

  #5 opened 5 years ago by embatty
  0