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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.
Quoting from <https://www.debian.org/doc/debian-policy/ch-controlfields.html#version>: > The lexical comparison is a comparison of ASCII values modified so that all the letters sort earlier than all the non-letters and so that a tilde sorts before anything, even the end of a part. For example, the following parts are in sorted order from earliest to latest: ~~, ~~a, ~, the empty part, a. Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Important! Template update for nf-core/tools v3.1.2
…into milestone_2.0.0
Important! Template update for nf-core/tools v3.2.0
Also updated MultiQC version in CHANGELOG.md and refreshed ro-crate-metadata.json.
Bring back merge commits from `master` to `dev`
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
…into milestone_2.0.0
Also pull the fix for the versions channel of last/train (see <nf-core/modules#7393>)
Milestone 2.0.0
tanyasarkjain
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Jan 31, 2025
jfy133
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Don't forget date change on the CHANGELOG!
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I would like to release
devas version2.0.0, to bring fixes and updates to users. Here is a copy of the changelog:v2.0.0 "Naga imo" - [January 31st, 2025]
Breaking changesparameters. The alignments ran with this pipeline will not be identical to
the ones from older versions.
Addedalignment/lastdbdirectory is not output anymore. It consumed space,is not usually needed for downstream analysis, and can be re-computed
identically if needed.
space. To keep this file, you can run the pipeline in
many-to-manymodewith the
--m2mparameter.--seedparameter allows for all the existing values in thelastdbprogram.
are now ignored.
--export_aln_tothat creates additional files containingthe alignments in a different format such as Axt, Chain, GFF or SAM.
FixedNs was corrected (#18).--lastal_paramsnow works as intended instead of being ignored (#22).Parameters--export_aln_toDependenciesLASTMultiQCPR 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).