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Release 2.8.0 #690
Release 2.8.0 #690
Commits on Nov 13, 2023
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Commits on Nov 14, 2023
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Merge pull request #661 from d4straub/bump-version-2.7.1-to-2.8.0dev
Bump version 2.7.1 to 2.8.0dev
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Commits on Nov 28, 2023
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Add params.qiime_ref_tax_custom in preparation of allowing custom qii…
…me database.
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Implementation of logic to handle a custom qiime2 reference database …
…stored in either a directory or a tarball.
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Add greengenes2 2022.10 to qiime ref databases.
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Add greengenes2022 to acceptable qiime_ref_taxonomy values.
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gzip does not operate on symbolic links unless forced or, as now, tol…
…d to emit result to stdout.
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Matthew Marshall committed
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Matthew Marshall committed
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Only perform collect if going to FORMAT_TAXONOMY_QIIME.
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Set into new channel when branching on ch_qiime_ref_taxonomy.£
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Try to unpack the database dir into component files using a module.
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Remove map wrapping the combine.
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Remove unpack in favour of map and filter.
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Glob results in list in all circumstances, check length instead.
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Merge remote-tracking branch 'upstream/dev' into greengenes_2022
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Add pull request link to changelog.
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Merge remote-tracking branch 'upstream/dev' into qiime2_custom_db
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Commits on Nov 29, 2023
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Update error message when passing both one of --qiime_ref_taxonomy or…
… --qiime_ref_tax_custom and --classifier.
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Update CHANGELOG.md with pull request number.
Co-authored-by: Daniel Straub <[email protected]>
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Add support for specifying two (possibly gzipped) files as --qiime_re…
…f_tax_custom.
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Only support providing two files separated by a comma.
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Fix split returns a String[] and we actually need an ArrayList.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db Conflicts: subworkflows/local/qiime2_preptax.nf workflows/ampliseq.nf
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Move ch_ref_database set into correct scope.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db
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Try using map to work through list of files.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db
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Can't call processes from inside maps.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db
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Fix outfile definition in GZIP_DECOMPRESS.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db
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Fix outfile definition in GZIP_DECOMPRESS.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db
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Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in…
…to qiime2_custom_db
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Add an early check that two paths are provided when providing a comma…
…-separated list.
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Make sure downstream is aware of new means of pointing to a qiime ref…
… db.
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Commits on Dec 1, 2023
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Improve error message clarity for ill-formed file.
Co-authored-by: Daniel Straub <[email protected]>
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Fix typo in error on --qiime_ref_paths form.
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Remove unneeded collect from FORMAT_TAXONOMY_QIIME invocation.
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Improve version tracking in PREPTAX.
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Add qiime_ref_tax_custom to testing in reftaxcustom nf-test.
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Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
…en-source-background-assets/ampliseq into qiime2_custom_db
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Commits on Dec 5, 2023
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Patch summary_report as it expects qiime_ref_taxonomy is set even whe…
…n it can be null due to classifier being passed.
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Commits on Dec 6, 2023
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Commits on Dec 7, 2023
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Merge pull request #672 from danclaytondev/dev
Update output docs for collapsed abundance tables
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Merge branch 'dev' into bugfix/summary_report
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Matthew Marshall committed
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Don't skip qiime while testing.
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Add a skip option for just downstream qiime analysis, but still perfo…
…rm qiime taxonomic classification.
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Merge branch 'qiime2_custom_db' of gitlab.stfc.ac.uk:omics/open-sourc…
…e-background-assets/ampliseq into qiime2_custom_db
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Skip qiime downstream in reftaxcustom.
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Fix path for testing tarball passed to --qiime_ref_tax_custom.
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Add snapshot of files coming from qiime2 taxonomy.
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Work towards a qiime_ref_tax_custom specific test.
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Matthew Marshall committed
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Sequence then taxonomy file for file pair to --qiime_ref_tax_custom.
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Clarify in help text of --qiime_ref_tax_custom the ordering of a file…
… pair.
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Update snapshots to include qiime2 in both correctly and add assertio…
…ns for qiime2.
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Make ordering of sequence and taxonomy files deterministic in case of…
… file pair.
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Fix filtering in file pair case.
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Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in…
…to qiime2_custom_db
Matthew Marshall committedDec 7, 2023 Configuration menu - View commit details
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Fix version mixing in --qiime_ref_taxonomy case.
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Update software version expectations for tests that no longer run QII…
…ME_PREPTAX.
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Remove assertions on dada2 tax and phyloseq files existing in test_qi…
…imecustom.
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Looks like qiime2 tax alignment is non-deterministic, just verify the…
… files it emits are emitted.
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Commits on Dec 8, 2023
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Co-authored-by: Daniel Straub <[email protected]>
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Make --skip_qiime_downstream help text clearer.
Co-authored-by: Daniel Straub <[email protected]>
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Remove assertion on qiime phyloseq file no longer produced.
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Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in…
…to qiime2_custom_db
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Commits on Dec 11, 2023
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Commits on Dec 12, 2023
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Merge pull request #675 from erikrikarddaniel/add-zehr-nifh
Add Zehr nifH database
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Merge pull request #673 from MatthewJM96/bugfix/summary_report
Fix qiime2 taxonomy part of summary report using unavailable information.
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Merge pull request #676 from d4straub/fix_phyloseq_input
Fix phyloseq input
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Commits on Dec 13, 2023
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Merge pull request #677 from jtangrot/update_sbdiexport
Update sbdiexport
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Commits on Dec 19, 2023
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Merge pull request #667 from MatthewJM96/qiime2_custom_db
Added QIIME2 custom reference database support.
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Merge pull request #679 from d4straub/fix-vsearch-cluster
Prevent masking low complexity regions by VSEARCH
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Merge pull request #680 from d4straub/fix-report
Improved pipeline summary report & error message
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Commits on Dec 20, 2023
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Merge pull request #681 from d4straub/add-dada_addspecies_allowmultip…
…le-dada_taxonomy_rc Add two parameters for taxonomic classification with DADA2
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Merge pull request #683 from d4straub/merging-template-updates-2-11
Merging template updates 2.11
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Commits on Dec 21, 2023
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Merge pull request #684 from nf-core/nf-core-template-merge-2.11.1
Important! Template update for nf-core/tools v2.11.1
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Commits on Jan 11, 2024
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Merge pull request #666 from MatthewJM96/greengenes_2022
Greengenes2 2022.10 Support
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Merge pull request #687 from d4straub/fix-FILTER_SSU-conda
fix conda package in FILTER_SSU
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Apply suggestions from code review
Co-authored-by: Till E. <[email protected]>
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Merge pull request #688 from d4straub/update-docs-tax-databases
Update docs, citations and usage with new taxonomic reference databases
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Merge pull request #689 from d4straub/bump-version-2.8.0
bump version to 2.8.0
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Commits on Jan 15, 2024
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Merge pull request #691 from d4straub/reviewer-comments-2-8-0
Reviewer comments 2.8.0
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