nf-core/magmap
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Version history
What’s Changed
- Add
proteins/magmap.proteins.faa.gz, a protein FASTA of all selected genomes - Add
Unassigned_NoFeatures/Unassigned_Ambiguitycolumns tooverall_stats.tsv.gz, and run FeatureCounts once per sample across all feature types - Faster start-up: the NCBI assembly summaries are only downloaded when
--indexesis given, and filtered in a process instead of the head process - Trim Galore! now runs with the default
process_mediumresources - Reject
--genomeinfoaccessions ending in a FASTA extension, and ignore FASTA extensions in--gtdbtk_metadata/--checkm_metadataidentifiers - Fix an empty methods-description bibliography in the MultiQC report and a crash on suppressed NCBI assemblies without
ftp_path - Replace the local
COLLECT_STATSandCOLLECT_FEATURECOUNTSmodules with shared nf-core components - Smaller, faster test suite
Thanks to @vagkaratzas, @nschan, @LouisLeNezet, @kathrynmurie and @danilodileo for substantial reviews, and to @leapicard, @dialvarezs, @Joon-Klaps, @maxulysse, @mashehu and @piplus2 for further reviews and contributions.
See CHANGELOG.md for the full changelog.
What’s Changed
- Fix saving of samtools output by @erikrikarddaniel in https://github.com/nf-core/magmap/pull/178
- Fix/bakta gff compatibility by @Laurenz0908 in https://github.com/nf-core/magmap/pull/181
- Template 3.5.2, Nextflow lint and version topic channels by @erikrikarddaniel in https://github.com/nf-core/magmap/pull/186
- Per sample genome sets by @erikrikarddaniel in https://github.com/nf-core/magmap/pull/188
- Add genome accno to counts tables by @erikrikarddaniel in https://github.com/nf-core/magmap/pull/189
- Pipeline lint release v1.1.0 by @danilodileo in https://github.com/nf-core/magmap/pull/190
- Review release 1.1.0 by @danilodileo in https://github.com/nf-core/magmap/pull/192
- fix github actions by @danilodileo in https://github.com/nf-core/magmap/pull/193
- Fix sample mode by @erikrikarddaniel in https://github.com/nf-core/magmap/pull/197
- Fix –indexes so it actually takes a list of indexes by @erikrikarddaniel in https://github.com/nf-core/magmap/pull/198
- Template update 4.0.2 by @danilodileo in https://github.com/nf-core/magmap/pull/199
- issue-200 by @danilodileo in https://github.com/nf-core/magmap/pull/201
- change NFT_WORKDIR to fix bug in nf-tests when conda is running by @danilodileo in https://github.com/nf-core/magmap/pull/202
- change NFT_WORKDIR by @danilodileo in https://github.com/nf-core/magmap/pull/203
- Fix pre-commit by @danilodileo in https://github.com/nf-core/magmap/pull/206
- updated prokka module by @danilodileo in https://github.com/nf-core/magmap/pull/207
- bypass prokka in nf-tests w conda by @danilodileo in https://github.com/nf-core/magmap/pull/208
- Magmap release v1.1.0 by @danilodileo in https://github.com/nf-core/magmap/pull/191
New Contributors
- @Laurenz0908 made their first contribution in https://github.com/nf-core/magmap/pull/181
Full Changelog: https://github.com/nf-core/magmap/compare/1.0.0...1.1.0
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