What’s Changed

• bump pipeline version to 1.2.0dev - LATÜRNICH by @subwaystation in #181
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #182
• fix wfmash v0.12.6 parameters and other bugs by @subwaystation in #183
• bump bcftools to 1.19 by @subwaystation in #184
• prepare 1.1.1 release by @subwaystation in #185
• 1.1.1 - LATÜRNICH by @subwaystation in #186

Full Changelog: 1.1.0…1.1.1

What’s Changed

• Update from Master to add DOI by @subwaystation in #137
• Update modules gfaffix, MultiQC, samtools/faidx by @subwaystation in #145
• Update vg deconstruct to v1.50.1 by @subwaystation in #146
• update smoothxg to v0.7.1 by @subwaystation in #147
• also put DRAW into MultiQC report by @subwaystation in #148
• another MultiQC fix by @subwaystation in #149
• Update modules odgi and wfmash by @subwaystation in #150
• fix wfmash_sparse_map parameter by @subwaystation in #152
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #153
• Add metric parameter suffixes by @heringerp in #155
• make the use of chunks explicit by @subwaystation in #160
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #163
• update modules by @subwaystation in #164
• Put functions within closure to evaluate them properly. by @adamrtalbot in #166
• update wfmash, multiqc by @subwaystation in #165
• fix delim bug by @subwaystation in #170
• Final pre-release 1.1.0 updates by @subwaystation in #175
• Prepare template 2.13 by @subwaystation in #177
• Important! Template update for nf-core/tools v2.13 by @nf-core-bot in #171
• prepare 1.1.0 release - Schmuddlweddr by @subwaystation in #178
• Some fixes for the release by @subwaystation in #180
• release 1.1.0 - Schmuddlweddr by @subwaystation in #179

New Contributors

• @heringerp made their first contribution in #155
• @adamrtalbot made their first contribution in #166

Full Changelog: 1.0.0…1.1.0

What’s Changed

• initial workflow and mini test running by @subwaystation in #3
• Add table of contributors to credits section by @heuermh in #1
• Fix test.config by @subwaystation in #5
• use FROM ghcr.io/pangenome/pggb
  by @heuermh in #4
• Fix merge conflicts from nf-core template v1.12 update by @heuermh in #7
• Important! Template update for nf-core/tools v1.12 by @nf-core-bot in #6
• Dockerfile by @subwaystation in #9
• Use nextflow.enable.dsl instead of nextflow.preview.dsl by @heuermh in #15
• Odgi stats consensus graphs by @subwaystation in #16
• fix pggb docker image to 20201125163549e465b0 by @subwaystation in #23
• extracted parameters from main.nf into nextflow.config by @Zethson in #24
• Fixed minimum NF badge in Readme by @Zethson in #25
• Multiqc by @subwaystation in #27
• Syncronize with pggb, more testing by @subwaystation in #29
• Template merge 112 by @Zethson in #31
• Important! Template update for nf-core/tools v1.12.1 by @nf-core-bot in #30
• update usage example by @subwaystation in #32
• reflect https://github.com/nf-core/tools/pull/812 by @subwaystation in https://github.com/nf-core/pangenome/pull/33
• update LH affiliations & fix EG affiliations by @Zethson in #34
• bump upstream Dockerfile to ghcr.io/pangenome/pggb:202012122000576ef861 by @heuermh in #35
• fixed —do_viz and —do_layout parameters by @subwaystation in #43
• updated Dockerfile, matched main.nf so that it can work with it by @subwaystation in #44
• the linting shouldn’t fail now by @subwaystation in #48
• Update with main fork by @subwaystation in #53
• Merging template updates by @subwaystation in #56
• Important! Template update for nf-core/tools v1.13.1 by @KevinMenden in #51
• This fixes Issue52: Sync with latest pggb by @subwaystation in #57
• This fixes #12 by @subwaystation in #58
• added flag to compress the output files by @AndreaGuarracino in #60
• Merging template updates by @subwaystation in #61
• better visualization management by @AndreaGuarracino in #62
• Dockerfile by @subwaystation in #64
• This updates the current prototype to match PGGB v0.2 by @subwaystation in #71
• Parallelize wfmash by @subwaystation in #72
• parallelize vg_deconstruct by @subwaystation in #73
• Pangenome/optional PAF input by @subwaystation in #83
• Wake me up when september ends by @subwaystation in #84
• seqwish_groovey_magic by @subwaystation in #85
• odgi sort/layout power up by @subwaystation in #86
• update Dockerfile to use the most recent biwflambda update by @subwaystation in #87
• diagnostic vizzz by @subwaystation in #88
• update wfmash for better short/medium sequence alignment by @subwaystation in #89
• integrate gfaffix bugfix and wfmash update via Dockerfile by @subwaystation in #90
• unchop the GFAFfixed graph by @subwaystation in #91
• update wfmash by @subwaystation in #93
• update to latest PGGB by @subwaystation in #94
• update Dockerfile by @subwaystation in #95
• update seqwish by @subwaystation in #96
• make the smoothxg step optional by @subwaystation in #98
• wfmashAlign: filter alignments -p x 0.8 by @subwaystation in #99
• use iterable smoothxg by @subwaystation in #100
• update Dockerfile by @subwaystation in #101
• update pggb docker image by @subwaystation in #102
• updage pggb in Dockerfile by @subwaystation in #104
• Community by @subwaystation in #105
• update pggb docker image by @subwaystation in #107
• the pipeline now works with all NXF versions by @subwaystation in #108
• draw 1D uncalled viz by @subwaystation in #109
• update pggb docker by @subwaystation in #112
• update pggb by @subwaystation in #113
• update Dockerfile to match most recent pggb updates by @subwaystation in #116
• update pggb docker image by @subwaystation in #118
• update pggb gfaffix by @subwaystation in #119
• update pggb Dockerfile by @subwaystation in #125
• This should bring in the current status of the pipeline - A brave new world! by @subwaystation in #128
• Output Documentation by @subwaystation in #129
• delete unused samplesheet files by @subwaystation in #130
• configure aws full scale test by @subwaystation in #131
• remove TODOs by @subwaystation in #133
• prepare 1.0.0 release by @subwaystation in #134
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #136
• 1.0.0 - Ratzupaltuff by @subwaystation in #135

New Contributors

• @subwaystation made their first contribution in #3
• @heuermh made their first contribution in #1
• @nf-core-bot made their first contribution in #6
• @Zethson made their first contribution in #24
• @KevinMenden made their first contribution in #51
• @AndreaGuarracino made their first contribution in #60

Full Changelog: https://github.com/nf-core/pangenome/commits/1.0.0