Milestone 2.0.0 #39
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Milestone 2.0.0 #39
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Release v1.1.0 that adds a new softmask parameter, to optionally keep original softmasking Merged despite linting fails, because failure is caused by template 3.0.0 release.
Release version 1.1.1
The files are not expected to be useful for downstream analyses and can be re-created identically if they were ever needed. Advanced users can also override the `publishDir` directive.
The alignment files take significant amount of disk space. Most users of the standard mode are only interested in the _one-to-one_ alignments. With that change, the intermediate alignment files are only kept in the `--m2m` mode, which is expected to be selected only by users interested in these alignments. Closes #30. Output is optional in the sense that one can always use `--m2m` to get the _many-to-one_ alignment even if not interested in the _one-to-many_.
Closes #29 When aligning a target to a large number of queries, it is sometimes impossible to know in advance if each of them is really alignable. Ignoring the error is a much better outcome than interrupting the pipeline and asking the user run the pipeline again after removing the problematic genomes from the sample sheet (or running again with a more sensitive seed). Errors caused by lack of memory etc. are still errors.
The update of LAST changes some alignment parameters, and therefore can change the pipeline results. Therefore this is a major upgrade.
…into milestone_2.0.0
Also updated MultiQC version in CHANGELOG.md and refreshed ro-crate-metadata.json.
jfy133
reviewed
Jan 30, 2025
jfy133
approved these changes
Jan 30, 2025
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
…into milestone_2.0.0
Also pull the fix for the versions channel of last/train (see <nf-core/modules#7393>)
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Version mixing and other issues fixed! |
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This PR is intended to prepare release 2.0.0. I am bumping the major version number because the update of the aligner modules cause the updated pipeline to output results that are not bit-identical to the previous version. I expect the other changes to be non-controversial, but I welcome comments or requests about the user interface.
Here is a copy of the changelog.
v2.0.0 "Naga imo" - [January 27th, 2025]
Backwards-incompatible changes
New features
alignment/lastdbdirectory is not output anymore. It consumed space, is not usually needed for downstream analysis, and can be re-computed identically if needed.many-to-manymode with the--m2mparameter.--seedparameter allows for all the existing values in thelastdbprogram.--export_aln_tothat creates additional files containing the alignments in a different format such as Axt, Chain, GFF or SAM.Bug fixes
Ns was corrected (#18).--lastal_paramsnow works as intended instead of being ignored (#22).PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).