The only change of this version: We revert module wfmash to v0.10.4, because the current releases are unstable, not documented, and I don’t understand how to set the parameters properly. It is currently unclear, when a new stable release will become available. @baozg or @AndreaGuarracino are evaluating.

Full Changelog: https://github.com/nf-core/pangenome/compare/1.1.2…1.1.2

What’s Changed

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

Full Changelog: https://github.com/nf-core/pangenome/compare/1.1.0…1.1.1

What’s Changed

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

New Contributors

• @heringerp made their first contribution in https://github.com/nf-core/pangenome/pull/155
• @adamrtalbot made their first contribution in https://github.com/nf-core/pangenome/pull/166

Full Changelog: https://github.com/nf-core/pangenome/compare/1.0.0…1.1.0

What’s Changed

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

New Contributors

• @subwaystation made their first contribution in https://github.com/nf-core/pangenome/pull/3
• @heuermh made their first contribution in https://github.com/nf-core/pangenome/pull/1
• @nf-core-bot made their first contribution in https://github.com/nf-core/pangenome/pull/6
• @Zethson made their first contribution in https://github.com/nf-core/pangenome/pull/24
• @KevinMenden made their first contribution in https://github.com/nf-core/pangenome/pull/51
• @AndreaGuarracino made their first contribution in https://github.com/nf-core/pangenome/pull/60

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