cbg-ethz/V-pipe

Issues

• `cyvcf2 = 0.30.11` leads to `ValueError: numpy.dtype size changed`

  #167 opened 2 months ago by GeertvanGeest
  6

• Workflow error from V-pipe dry run

  #160 opened 4 months ago by robertsap
  3

• Default deconvolution config is missing

  #161 opened 4 months ago by GeertvanGeest
  0

• How to run analysis for single-end reads

  #61 opened 5 years ago by zuber-bioinfo
  3

• Setting VILOCA --windowsize parameter using v-pipe config file not possible

  #157 opened 6 months ago by anikajohn
  0

• Snakemake standardized usage

  #151 opened 7 months ago by uniqueg
  0

• Problem in the deconvolution step

  #148 opened a year ago by Xuyen21
  4

• Activating snv in sars tutorial leads to error

  #146 opened 2 years ago by schlaepferp
  2

• Snakemake dry run 404

  #147 opened a year ago by helmotw
  9

• vpipe broken? ModuleNotFoundError: No module named 'pandas'

  #145 opened 2 years ago by schlaepferp
  2

• frameshift_deletion_checks, simBench & Haplotype callers

  #132 opened 2 years ago by dimitris-karapliafis
  6

• [UX issue] multiple GFF

  #134 opened 2 years ago by DrYak
  1

• Error in rule hmm_align: HIV in Vpipe

  #138 opened 2 years ago by vfdiamante
  2

• predicthaplo does not work on sars-cov-2 tutorial

  #135 opened 2 years ago by Masterxilo
  1

• Missing input files for rule generate_web_visualization

  #139 opened 2 years ago by carlottaolivero
  0

• Warning: cannot detect conda environment

  #100 opened 4 years ago by med-ss20
  4

• hiv-tutorial fails with haplotype_reconstruction: savage, and SAVAGE command output is dumped into terminal instead of log

  #137 opened 2 years ago by Masterxilo
  0

• hiv-tutorial works with haploclique, but fails with predicthaplo

  #136 opened 2 years ago by Masterxilo
  0

• [UX issue] unknown keywords in config file

  #133 opened 2 years ago by DrYak
  1

• Conflict in quality_assurance.smk with custom datadir-path

  #127 opened 2 years ago by LaraFuhrmann
  0

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

  #124 opened 3 years ago by thomasbtf
  1

• Warning: All reads at position 4045 in the same reverse orientation ?

  #126 opened 3 years ago by Vinoy-UKHSA
  1

• Getting snake error

  #120 opened 3 years ago by dstcr
  23

• please document haploclique.extra_parameters

  #122 opened 3 years ago by Masterxilo
  3

• Running with tutorial dataset giving all empty file

  #119 opened 3 years ago by wasimbt
  6

• ./vpipe --dryrun error

  #80 opened 4 years ago by ibseq
  11

• wrong url for release download in quick install

  #114 opened 3 years ago by Masterxilo
  2

• The order of jobs does not reflect the order of execution. Any help?

  #107 opened 3 years ago by carlottaolivero
  1

• Provide Dockerfile & prebuilt/automatically built container image

  #21 opened 6 years ago by Masterxilo
  8

• ShoRAh: list index out of range

  #64 opened 3 years ago by stefanches7
  1

• error for assigning config file by snakemake option

  #89 opened 4 years ago by vicfabienne
  3

• KeyError: <rule name>

  #98 opened 3 years ago by DrYak
  1

• Haplotype percentage or frequency estimation

  #101 opened 3 years ago by poursalavati
  0

• shorah sampling status

  #87 opened 4 years ago by snaketron
  1

• shorah output in vcf for all samples

  #96 opened 4 years ago by ibseq
  2

• posterior values using lofreq rule?

  #88 opened 4 years ago by vicfabienne
  2

• Solved. Verification error.

  #92 opened 4 years ago by weihongqi
  1

• Conda not installed in standard location

  #86 opened 4 years ago by jeffkimbrel
  6

• threading question

  #85 opened 4 years ago by rsettlage
  7

• Primers trimming

  #82 opened 4 years ago by chadisaad
  1

• Error in rule generate_web_visualization

  #76 opened 4 years ago by PegahDan
  1

• Cause of (shorah_regions) error?

  #79 opened 4 years ago by snaketron
  2

• lofreq environment file contains unsolvable conflicts

  #63 opened 4 years ago by stefanches7
  3

• Vicuna error

  #24 opened 4 years ago by mhopken
  8

• ResolvePackageNotFound: - savage=0.4.2

  #69 opened 4 years ago by Jamesped
  2

• got stuck in this rule convert_to_ref, convert_reference did not work

  #70 opened 4 years ago by Jamesped
  2

• ImportError: Bio.Alphabet has been removed from Biopython

  #68 opened 4 years ago by yvanw
  2

• Compatible execution of jar files

  #11 opened 5 years ago by sposadac
  0

• Have a wiki homepage like other repositories

  #20 opened 5 years ago by Masterxilo
  1

• Errors on Snakemake 5.x

  #17 opened 6 years ago by DrYak
  0