CRG-CNAG/CalliNGS-NF

Issues

• ERROR: Input files reference and features have incompatible contigs

  #36 opened 2 years ago by kyle-lk
  0

• Operator `phase` is deprecated

  #35 opened 2 years ago by HudoGriz
  0

• Process `ASE_KNOWNSNPS (SAMPLE123XYZ)` terminated with an error exit status (2) (More then one variant context at position: chr3:XXXXXXX)

  #33 opened 2 years ago by SINGHVJ-Bio
  2

• will there be a nf of dna variant calling which need paired samples

  #29 opened 3 years ago by asmlgkj
  0

• Documentation issue?

  #32 opened 3 years ago by pieterlukasse
  2

• denylisted genome file

  #31 opened 3 years ago by okeyoallan
  0

• Could not build fai index genome.fa.fai

  #30 opened 3 years ago by Jokendo-collab
  0

• The on-the-fly two-pass option could be used to avoid the genome regeneration step

  #26 opened 3 years ago by kojix2
  3

• mm39 variants / black list

  #23 opened 3 years ago by sarahbonnin
  4

• Whether do not generate star index if provide directly?

  #20 opened 4 years ago by RyanYip-Kat
  1

• could not execute mkdir

  #22 opened 3 years ago by sean1sun
  1

• Process POST_PROCESS_VCF failes when order of chromosomes in result.DP8.vcf differs from that in the GRCm38/Annotation/Variation/Mus_musculus.vcf

  #21 opened 3 years ago by dylanht
  0

• Reading single end reads

  #19 opened 4 years ago by Jokendo-collab
  4

• The genomeDir dir name is confusing

  #13 opened 4 years ago by pditommaso
  0

• containerOverrides for AWS BATCH

  #8 opened 5 years ago by Dharmendra-G-1
  1

• picard.jar not found

  #10 opened 4 years ago by robertobarrero
  1

• GATK4 branch does not require separate Picard

  #14 opened 4 years ago by jdwheaton
  3

• samtools: command not found

  #9 opened 4 years ago by cailiangliang765
  3

• Implement support for GATK4

  #4 opened 4 years ago by pditommaso
  17

• suggest adding docker runOptions to nextflow.config

  #16 opened 4 years ago by jayoung
  1

• Cannot locate GATK.jar file

  #17 opened 4 years ago by Jokendo-collab
  1

• Error: Unable to access jarfile /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar

  #18 opened 4 years ago by Jokendo-collab
  1

• Using Single end data

  #11 opened 5 years ago by benkraj
  5

• Error in SplitNCigarReads step

  #5 opened 5 years ago by slagtermaarten
  3

• Variant calling step failing when using process scratch

  #3 opened 7 years ago by pditommaso
  1

• Typo in the title of the flow-chart picture.

  #2 opened 7 years ago by pditommaso
  0