nf-core/raredisease

Issues

• Test+Docker profile fails: Can't locate object method "cdna_coords"

  #611 opened a month ago by Oliversinn
  6

• ERROR ~ while scanning a simple key

  #603 opened 2 months ago by sitems
  3

• Split deepvariant pipeline

  #614 opened a month ago by fa2k
  1

• gnomAD v4.1 SV database contains mix of SV and CNV - svdb problem

  #615 opened a month ago by fa2k
  0

• Empty VCF file fails in genmod score

  #613 opened a month ago by fa2k
  1

• Add option to take a whitelist of variants

  #469 opened a month ago by jemten
  2

• Help with figuring out if error is pipeline or HPC related

  #612 opened a month ago by hrydbeck
  1

• Test+Docker profile fails: "The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine."

  #590 opened 2 months ago by sitems
  5

• Allow multiple unrelated cases/families in samplesheet.csv

  #604 opened 2 months ago by sitems
  1

• Option to publish GVCFs

  #602 opened 2 months ago by sitems
  2

• Mismatch with new DNAScope ML model format

  #568 opened 4 months ago by Jakob37
  3

• Update CADD to version 1.7

  #513 opened 8 months ago by jemten
  2

• filter_vep broken with hg38

  #599 opened 2 months ago by fellen31
  1

• Add default support for haploid variant calls

  #596 opened 2 months ago by jemten
  2

• Allow 'lane' in samplesheet.csv to be String type (as in e.g. sarek)

  #591 opened 2 months ago by sitems
  4

• Stub run (and regular run) crashes on PEDDY

  #566 opened 2 months ago by Jakob37
  3

• `vep_plugin_files` listed as optional parameter but pipeline won't run without it

  #593 opened 2 months ago by fellen31
  1

• Test+Docker profile fails: "ValueError: `call_variants_outputs` did not pass sanity check."

  #592 opened 2 months ago by sitems
  1

• publishDir mode missing in raredisease.config for processes FASTQC and CREATE_PEDIGREE_FILE

  #583 opened 3 months ago by irliampa
  1

• bash: singularity: command not found

  #575 opened 4 months ago by hrydbeck
  5

• destination filesystem does not support xattrs

  #565 opened 4 months ago by hrydbeck
  3

• Container for get_chrom_sizes doesn't work

  #567 opened 4 months ago by Lucpen
  1

• Bigtools

  #564 opened 4 months ago by ramprasadn
  0

• https://ai.marrvel.org / how to integrate to Scout and our analysis?

  #560 opened 5 months ago by fulyataylan
  5

• Join error ME_INDEX_SPLIT_ALIGNMENT

  #542 opened 5 months ago by fa2k
  10

• Error when 'other' is given as gender

  #549 opened 5 months ago by sima-r
  2

• could not open image Script8C84027CBF0BFB90846176A9D9C58EDE@30624c7

  #540 opened 5 months ago by hrydbeck
  1

• ped file cannot be created when outdir is an s3 path

  #554 opened 5 months ago by evanfloden
  1

• Multi-allelic indel sites don't get CADD scores for all alleles

  #544 opened 5 months ago by fa2k
  0

• Nextflow version requirement (documentation)

  #539 opened 6 months ago by fa2k
  1

• Error_during_installation

  #537 opened 7 months ago by vishramt7
  10

• GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls?

  #535 opened 7 months ago by bnjvrjnke
  2

• URGENT: pin nf-validation version

  #520 opened 7 months ago by nvnieuwk
  2

• Implementation of BWA

  #519 opened 8 months ago by lfearnley
  2

• manta path error

  #480 opened 9 months ago by egenomics
  14

• Confirm that the gens workflow works as intended

  #494 opened 8 months ago by jemten
  2

• Standardize naming of outfiles

  #492 opened 8 months ago by jemten
  0

• Add Rhocall viz

  #496 opened 8 months ago by jemten
  1

• rtgtools: Add truth set filtered by bait set for WES samples

  #514 opened 8 months ago by peterpru
  0

• filter_vep options

  #498 opened 8 months ago by jemten
  1

• Option to use different variant consequence priority list for SNV and SVs

  #509 opened 8 months ago by ramprasadn
  1

• Downsample MT alignment file for IGV

  #497 opened 9 months ago by jemten
  1

• Chromograph coverage

  #495 opened 9 months ago by jemten
  1

• update genmod to version 3.8.2

  #486 opened 9 months ago by jemten
  1

• Save bam files from exapnsionhunter

  #493 opened 9 months ago by jemten
  0

• Add stubs to FASTP process

  #467 opened 9 months ago by Jakob37
  2

• Remove hardcoded platform

  #478 opened 9 months ago by jemten
  1

• Switch to nf-core version of VEP

  #477 opened 9 months ago by jemten
  1

• Validate svdb query database input

  #473 opened 9 months ago by jemten
  1

• Tag each SNVs with the variant caller that was used

  #466 opened 9 months ago by jemten
  0