moiexpositoalonsolab/grenepipe

Issues

• SLURM cluster_config not recognized

  #51 opened 2 months ago by meixilin
  3

• Workflow fails with contig-group-size != 0

  #52 opened a month ago by lczech
  1

• restrict-regions and short contigs

  #36 opened 10 months ago by RvV1979
  4

• not sure what the issue is

  #49 opened 2 months ago by Leovar101
  12

• --rerun-incomplete flag repeat mapping step for all samples

  #50 opened 2 months ago by athenasyarifa
  6

• permission denied error

  #48 opened 2 months ago by Leovar101
  5

• mamba is difficult to install in grenepipe environment

  #40 opened 4 months ago by wangshuangyi
  6

• another type of error

  #47 opened 2 months ago by ospfsg
  11

• Feature Request: Download reference genome and known variation

  #41 opened 2 months ago by pettyalex
  2

• Make "trimming-tool" optional

  #35 opened 2 months ago by coolkom
  4

• a new type of error

  #45 opened 6 months ago by ospfsg
  2

• problem with dedup

  #44 opened 6 months ago by ospfsg
  4

• a new type of error

  #46 opened 6 months ago by ospfsg
  1

• greenepipe run error

  #43 opened 6 months ago by ospfsg
  5

• config file

  #42 opened 6 months ago by ospfsg
  5

• merging calls from multiple pipeline runs?

  #39 opened 9 months ago by RvV1979
  2

• Write full executed command for each step to log files for reproducibility

  #38 opened 9 months ago by uzbit
  3

• ModuleNotFoundError: No module named 'chardet'

  #37 opened 9 months ago by RvV1979
  2

• MissingRuleException

  #31 opened a year ago by mrese001
  13

• GRENEPIPE v12.1

  #34 opened a year ago by mrese001
  5

• java.lang.OutOfMemoryError: Java heap space

  #33 opened a year ago by RvV1979
  2

• PID error

  #32 opened a year ago by Kkaholoaa
  9

• Error running toy example

  #30 opened a year ago by celianeto
  6

• Error in mapping on cluster

  #27 opened 2 years ago by AxelVaillant
  6

• Versions specified in conda env files and snakemake wrappers lead to conflicts/are not available

  #25 opened 2 years ago by akriese
  11

• Picard environment not created

  #11 opened 2 years ago by henriquevf
  8

• threads for bwa-mem2 via slurm

  #29 opened 2 years ago by RvV1979
  2

• bwa-mem2 "{tmp}.0000.bam": File exists

  #28 opened 2 years ago by RvV1979
  5

• config file error

  #26 opened 2 years ago by BFeldmeyer
  5

• Run snakemake on Cluster

  #23 opened 2 years ago by orangelc1221
  3

• Conda installation error

  #24 opened 2 years ago by Samarth-T-Setty
  7

• CondaMemoryError when creating conda envs in cluster

  #22 opened 2 years ago by orangelc1221
  3

• Updating run with new reads

  #14 opened 3 years ago by Brent-Saylor-Canopy
  12

• BaseRecalibrator error - needs more readgroup info?

  #20 opened 2 years ago by mvdloosdrecht
  2

• feature request: pass local reference genome database to snpEff

  #13 opened 2 years ago by bensprung
  2

• snpEff download directory only works with a trailing slash

  #12 opened 2 years ago by bensprung
  3

• Call variants being rerun when adding new samples

  #18 opened 3 years ago by Brent-Saylor-Canopy
  3

• Error while running example

  #21 opened 2 years ago by andrewSharo
  6

• vcf file with all positions

  #6 opened 2 years ago by florianhahn87
  6

• Change link in wiki

  #19 opened 3 years ago by Tatianabellagio
  1

• Error in picard_collectmultiplemetrics

  #16 opened 3 years ago by Brent-Saylor-Canopy
  4

• freebayes causes early error about number of threads

  #17 opened 3 years ago by bensprung
  12

• support for haploid genomes?

  #15 opened 3 years ago by bensprung
  8

• FastQC on one set of reads only

  #10 opened 3 years ago by bensprung
  7

• CollectMultipleMetrics: there is no package called ‘tidyverse’

  #9 opened 3 years ago by bensprung
  6

• Too many jobs created if reference genome has a large number of contigs

  #8 opened 3 years ago by J-Wall
  2

• Add option to use bwa-mem2 for mapping

  #7 opened 3 years ago by J-Wall
  3

• No module named 'numpy.core._multiarray_umath'

  #5 opened 3 years ago by bensprung
  14

• separate output files if running on multiple files

  #4 opened 3 years ago by florianhahn87
  10

• Issues during variant calling

  #3 opened 3 years ago by florianhahn87
  2