nf-core/pangenome issues and pull requests

#160 - make the use of chunks explicit

Pull Request - State: closed - Opened by subwaystation about 1 year ago - 1 comment

#159 - update module GFAFFIX

Issue - State: open - Opened by subwaystation about 1 year ago
Labels: enhancement

#158 - automatically detect the number of input haplotypes

Issue - State: open - Opened by subwaystation about 1 year ago
Labels: enhancement

#157 - Update vg/deconstruct Docs and CI

Issue - State: open - Opened by subwaystation about 1 year ago
Labels: enhancement

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

Issue - State: open - Opened by subwaystation about 1 year ago - 3 comments
Labels: enhancement

#155 - Add metric parameter suffixes

Pull Request - State: closed - Opened by heringerp over 1 year ago - 1 comment

#154 - fix 4 out of 5 linting errors

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 2 comments

#153 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 4 comments

#152 - fix wfmash_sparse_map parameter

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#151 - Integrate `panacus` as a quantitative quality control tool and pangenome growth curve generator

Issue - State: open - Opened by subwaystation over 1 year ago
Labels: enhancement

#150 - Update modules odgi and wfmash

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#149 - another MultiQC fix

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#148 - also put DRAW into MultiQC report

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#147 - update smoothxg to v0.7.1

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#146 - Update `vg deconstruct` to v1.50.1

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#145 - Update modules gfaffix, MultiQC, samtools/faidx

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 2 comments

#144 - Update `MultiQC` to v1.15

Issue - State: closed - Opened by subwaystation over 1 year ago
Labels: enhancement

#143 - Update `gfaffix` to v0.1.5

Issue - State: closed - Opened by subwaystation over 1 year ago
Labels: enhancement

#142 - Update `smoothxg` to hopefully v0.7.1

Issue - State: closed - Opened by subwaystation over 1 year ago - 3 comments
Labels: enhancement

#141 - Update `wfmash` to v0.10.5

Issue - State: closed - Opened by subwaystation over 1 year ago - 2 comments
Labels: enhancement

#140 - Update `vg deconstruct` to v1.50.1

Issue - State: closed - Opened by subwaystation over 1 year ago - 1 comment
Labels: enhancement

#139 - Check if input sequence identifiers follow the PanSN-Spec

Issue - State: open - Opened by subwaystation over 1 year ago
Labels: enhancement

#138 - Issue with test profile

Issue - State: open - Opened by DPI-NZ over 1 year ago - 10 comments
Labels: bug

#137 - Update from Master to add DOI

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#136 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#135 - 1.0.0 - Ratzupaltuff

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 21 comments

#134 - prepare 1.0.0 release

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#133 - remove TODOs

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#132 - update samtools faidx moduels

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 2 comments

#131 - configure aws full scale test

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#130 - delete unused samplesheet files

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#129 - Output Documentation

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 4 comments

#128 - This should bring in the current status of the pipeline - A brave new world!

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 2 comments

#127 - DO NOT MERGE! - Mersch 2.8

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 2 comments

#126 - Template update for nf-core/tools version 2.8

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#125 - update pggb Dockerfile

Pull Request - State: closed - Opened by subwaystation over 1 year ago - 1 comment

#124 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#123 - Update wfmash to 0.10.3

Issue - State: closed - Opened by subwaystation almost 2 years ago - 1 comment
Labels: enhancement

#122 - Update seqwish to 0.7.9

Issue - State: closed - Opened by subwaystation almost 2 years ago - 1 comment
Labels: enhancement

#121 - Use `grabix` to detect compression mode of FASTA input.

Issue - State: open - Opened by subwaystation almost 2 years ago
Labels: enhancement

#120 - Support metric parameter suffixes

Issue - State: closed - Opened by subwaystation almost 2 years ago - 1 comment
Labels: enhancement

#119 - update pggb gfaffix

Pull Request - State: closed - Opened by subwaystation almost 2 years ago - 1 comment

#118 - update pggb docker image

Pull Request - State: closed - Opened by subwaystation almost 2 years ago - 1 comment

#117 - Won't accept sample sheet.csv

Issue - State: closed - Opened by SarahBeecroft almost 2 years ago - 2 comments
Labels: bug

#116 - update Dockerfile to match most recent pggb updates

Pull Request - State: closed - Opened by subwaystation almost 2 years ago - 2 comments

#115 - DO NOT MERGE! A brave new world

Pull Request - State: closed - Opened by subwaystation almost 2 years ago - 6 comments

#114 - A brave new world

Pull Request - State: closed - Opened by subwaystation almost 2 years ago

#113 - update pggb

Pull Request - State: closed - Opened by subwaystation almost 2 years ago - 1 comment

#112 - update pggb docker

Pull Request - State: closed - Opened by subwaystation almost 2 years ago - 1 comment

#111 - Allow `vg deconstruct` in community mode

Issue - State: closed - Opened by subwaystation almost 2 years ago - 2 comments
Labels: enhancement

#110 - Emit the 2D layout also in TSV format

Issue - State: closed - Opened by subwaystation almost 2 years ago - 2 comments
Labels: enhancement

#109 - draw 1D uncalled viz

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#108 - the pipeline now works with all NXF versions

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#107 - update pggb docker image

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#106 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#105 - Community

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#104 - updage pggb in Dockerfile

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#103 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#102 - update pggb docker image

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#101 - update Dockerfile

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#100 - use iterable smoothxg

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#99 - wfmashAlign: filter alignments -p x 0.8

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#98 - make the smoothxg step optional

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 3 comments

#97 - Perform sequence partitioning for massive parallelization

Issue - State: closed - Opened by subwaystation about 2 years ago - 1 comment
Labels: enhancement

#96 - update seqwish

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#95 - update Dockerfile

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#94 - update to latest PGGB

Pull Request - State: closed - Opened by subwaystation about 2 years ago - 1 comment

#93 - update wfmash

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 2 comments

#92 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#91 - unchop the GFAFfixed graph

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 1 comment

#90 - integrate gfaffix bugfix and wfmash update via Dockerfile

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 1 comment

#89 - update wfmash for better short/medium sequence alignment

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 1 comment

#88 - diagnostic vizzz

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 2 comments

#87 - update Dockerfile to use the most recent biwflambda update

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 1 comment

#86 - odgi sort/layout power up

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 1 comment

#85 - seqwish_groovey_magic

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 3 comments

#84 - Wake me up when september ends

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 2 comments

#83 - Pangenome/optional PAF input

Pull Request - State: closed - Opened by subwaystation over 2 years ago - 3 comments

#82 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#81 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#80 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#79 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#78 - Important! Template update for nf-core/tools v2.3.1

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#77 - Important! Template update for nf-core/tools v2.3

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 2 comments

#76 - Documentation

Issue - State: closed - Opened by subwaystation almost 3 years ago - 2 comments
Labels: documentation

#75 - Important! Template update for nf-core/tools v2.2

Pull Request - State: closed - Opened by nf-core-bot about 3 years ago - 1 comment

#74 - Test data for the pipeline

Issue - State: closed - Opened by subwaystation about 3 years ago - 2 comments
Labels: enhancement

#73 - parallelize vg_deconstruct

Pull Request - State: closed - Opened by subwaystation about 3 years ago

#72 - Parallelize wfmash

Pull Request - State: closed - Opened by subwaystation about 3 years ago - 1 comment

#71 - This updates the current prototype to match PGGB v0.2

Pull Request - State: closed - Opened by subwaystation about 3 years ago - 2 comments

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

Issue - State: closed - Opened by subwaystation over 3 years ago - 12 comments
Labels: enhancement

#69 - Important! Template update for nf-core/tools v2.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#68 - Important! Template update for nf-core/tools v2.0.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#67 - Important! Template update for nf-core/tools v2.0

Pull Request - State: closed - Opened by KevinMenden over 3 years ago - 1 comment

#66 - Important! Template update for nf-core/tools v1.14

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#65 - pipeline has no release, bu no UNDER CONSTRUCTION warning

Issue - State: closed - Opened by maxulysse over 3 years ago - 1 comment
Labels: bug

#64 - Dockerfile

Pull Request - State: closed - Opened by subwaystation almost 4 years ago

#63 - Pgge

Pull Request - State: closed - Opened by subwaystation almost 4 years ago

#62 - better visualization management

Pull Request - State: closed - Opened by AndreaGuarracino almost 4 years ago - 1 comment

#61 - Merging template updates

Pull Request - State: closed - Opened by subwaystation almost 4 years ago

GitHub / nf-core/pangenome issues and pull requests