nf-core/pangenome

Issues

• Command 'ps' required by nextflow to collect task metrics cannot be found

  #207 opened 3 months ago by chenhijy
  3

• GFA to rGFA problem

  #206 opened 4 months ago by mictadlo
  5

• wfmash step to speed up

  #205 opened 5 months ago by OZTaekOppa
  6

• Use `grabix` to detect compression mode of FASTA input.

  #121 opened 2 years ago by subwaystation
  0

• Adding input files for Panache

  #197 opened 9 months ago by mictadlo
  3

• Adding jbrowse visualization

  #196 opened 9 months ago by mictadlo
  4

• How to use Bgzip

  #167 opened 9 months ago by mictadlo
  32

• Update tests so that nf-test can run the tests

  #187 opened 9 months ago by subwaystation
  0

• Compile SMOOTHXG for several kinds of SIMD flavours

  #190 opened 9 months ago by subwaystation
  0

• Towards IMplicit Pangenome Graph Construction Tools

  #189 opened 9 months ago by subwaystation
  0

• Integrate `panacus` as a quantitative quality control tool and pangenome growth curve generator

  #151 opened a year ago by subwaystation
  0

• Issue with test profile

  #138 opened 9 months ago by DPI-NZ
  11

• assume pansn-spec in wfmash parameters to enfoce lower-triangular mapping

  #156 opened a year ago by subwaystation
  4

• Update vg/deconstruct Docs and CI

  #157 opened 9 months ago by subwaystation
  1

• wfmash killed

  #168 opened 9 months ago by mictadlo
  10

• URGENT: pin nf-validation version

  #172 opened 9 months ago by nvnieuwk
  3

• update module GFAFFIX

  #159 opened 10 months ago by subwaystation
  3

• Clean up stale git branches

  #173 opened 10 months ago by heuermh
  6

• parallelization over chromosomes

  #37 opened 3 years ago by subwaystation
  4

• Won't accept sample sheet.csv

  #117 opened 2 years ago by SarahBeecroft
  4

• automatically detect the number of input haplotypes

  #158 opened a year ago by subwaystation
  0

• Support metric parameter suffixes

  #120 opened a year ago by subwaystation
  1

• Update `wfmash` to v0.10.5

  #141 opened a year ago by subwaystation
  2

• Update `smoothxg` to hopefully v0.7.1

  #142 opened a year ago by subwaystation
  3

• Update `vg deconstruct` to v1.50.1

  #140 opened a year ago by subwaystation
  1

• Update `gfaffix` to v0.1.5

  #143 opened a year ago by subwaystation
  0

• Update `MultiQC` to v1.15

  #144 opened a year ago by subwaystation
  0

• Check if input sequence identifiers follow the PanSN-Spec

  #139 opened a year ago by subwaystation
  0

• Allow `vg deconstruct` in community mode

  #111 opened 2 years ago by subwaystation
  2

• Emit the 2D layout also in TSV format

  #110 opened 2 years ago by subwaystation
  2

• Update seqwish to 0.7.9

  #122 opened 2 years ago by subwaystation
  1

• Update wfmash to 0.10.3

  #123 opened 2 years ago by subwaystation
  1

• Modules required for the nf-core compliant DSL2 implementation of the pipeline

  #70 opened 2 years ago by subwaystation
  12

• add pgge

  #38 opened 2 years ago by subwaystation
  2

• Perform sequence partitioning for massive parallelization

  #97 opened 2 years ago by subwaystation
  1

• fastify pangenome generation

  #36 opened 4 years ago by subwaystation
  1

• Test data for the pipeline

  #74 opened 2 years ago by subwaystation
  2

• Documentation

  #76 opened 2 years ago by subwaystation
  2

• Pangenome: Convert parameter docs to JSON schema documentation

  #49 opened 3 years ago by apeltzer
  1

• pipeline has no release, bu no UNDER CONSTRUCTION warning

  #65 opened 3 years ago by maxulysse
  1

• pangenome pipeline choking on multiple inputs

  #39 opened 3 years ago by dbrami
  2

• Update odgiViz and odgiDraw

  #28 opened 4 years ago by subwaystation
  1

• Add the possbility to compress the output files with pigz

  #55 opened 4 years ago by subwaystation
  0

• Sync with latest pggb

  #52 opened 4 years ago by subwaystation
  0

• Resolve Template Update PR

  #54 opened 4 years ago by subwaystation
  1

• markdownlint argument -c/--config ignores any input

  #47 opened 4 years ago by subwaystation
  0

• Issues with odgibuild

  #42 opened 4 years ago by dbrami
  4

• periods in name break odgibuild logic

  #41 opened 4 years ago by dbrami
  3

• way to modify number of threads for edyeet for pangenome pipeline

  #40 opened 4 years ago by dbrami
  1

• Sync to pggb a177033ddc3f73ff84d32b7ef24480f075dce3a4

  #26 opened 4 years ago by subwaystation
  1