Milestone 2.2.0 #66
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Milestone 2.2.0 #66
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This is in preparation for CRAM support.
2.1.0 release
FASTA_BGZIP_INDEX_DICT_SAMTOOLS is a subworkflow that takes a FASTA file regardless of its compression, and returns it BGZIPped together with index files needed to sort the alignments and a sequence dictionary needed to ensure that alignments of different _queries_ to the same _target_ can be merged later.
Pushing this commit now to trigger a new CI run of the nf-core branch protection. This said, multiqc_assemblyscan_plot_data combines one file per _query_ genome, and removing the `tag` ensure that the list of file names does not clutter the screen when monitoring the pipeline run. The nf-core MultiQC module also does not have a `tag`. Closes #64
jfy133
approved these changes
May 22, 2025
subworkflows/local/fasta_bgzip_index_dict_samtools/tests/main.nf.test
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Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
…into milestone_2.2.0
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Thanks a lot for the very useful comments. I have added credit to Samtools and opened an issue about the diagram (#68) |
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This PR adds
bamandcramto the list of supported export formats. A new subworkflow takes care of ensuring that the genome file is appropriately compressed and indexed for CRAM encoding and to support the user running BAM/CRAM indexing commands later. A sequence dictionary is computed, and will be useful in a future update oflast/mafconvert(PR under review).Other updates preparing the 2.2.0 release will follow, but I thought that it would be useful to review this bunch of commits separately. In particular I welcome critical comments on how I manage the optional run of the subworkflow in
workflows/pairgenomealign.nf.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).