Releases: nf-core/pangenome
Releases · nf-core/pangenome
pangenome 1.1.2 - canguro
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: 1.1.2...1.1.2
Contributors
baozg and AndreaGuarracino
Assets 2
pangenome 1.1.1 - LATÜRNICH
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
Contributors
subwaystation and nf-core-bot
Assets 2
pangenome 1.1.0 - Schmuddlweddr
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 deconstructto 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
Contributors
subwaystation, adamrtalbot, and 2 other contributors
Assets 2
pangenome 1.0.0 - Ratzupaltuff
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:latest 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 nf-core/tools#812 by @subwaystation in #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
Contributors
heuermh, subwaystation, and 4 other contributors