Version history
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 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