The pipeline was extensively restructured to better comply with nf-core guidelines.
New functionality:
- Bins support: Bins can now be uploaded to ENA with all mandatory metadata.
- Pre-binned results support: Pre-generated results from CONCOCT, MaxBin, and/or MetaBAT can be provided as input via the samplesheet.
- Integrated download step: A download step was added, allowing the pipeline to run without pre-downloading reads and assemblies.
- MAGs and bins upload: An upload step for MAGs and bins was added. A Webin account is required.
Changes:
- The directory-path structure used to reference the genome was modified.
Other updates:
- Several pipeline steps required cleanup and reorganization of input arguments.
What's Changed
- Specified temp dirs to solve "OSError: AF_UNIX path too long" by @Ge94 in #43
- add step for download by @KateSakharova in #44
- Specified temp dirs to solve the OSError: AF_UNIX path too long in cat by @jmattock5 in #47
- Use binette for bin refining instead of mgbinrefinder by @ochkalova in #45
- Comment out multiqc and refine readme by @Ge94 in #46
- Feature/retry upload by @KateSakharova in #42
- Feature/update gtdbtk by @KateSakharova in #48
- support for new ref-system by @KateSakharova in #51
- Upload bins to ENA during pipeline run by @ochkalova in #50
- Feature/allow bins input by @KateSakharova in #29
- Update reference genome index path for bwa-mem2 by @ochkalova in #56
- fixes after testing new ggp by @KateSakharova in #57
- Add --force option to CAT command by @Ales-ibt in #59
- add retries to MAG_CLEANUP_CAT by @KateSakharova in #60
- Develop by @KateSakharova in #58
New Contributors
- @Ge94 made their first contribution in #43
- @jmattock5 made their first contribution in #47
- @ochkalova made their first contribution in #45
Full Changelog: 1.2.0...1.3.0
Contributors
Ge94, Ales-ibt, and 3 other contributors