Added QIIME2 custom reference database support.#667

Merged

d4straub merged 65 commits intonf-core:devfrom MatthewJM96:qiime2_custom_db

Dec 19, 2023

+310-27

Commits on Jun 26, 2023

Merge pull request nf-core#601 from nf-core/dev
d4straub
authored

Commits on Jun 27, 2023

Merge pull request nf-core#604 from nf-core/dev
d4straub
authored

Commits on Oct 19, 2023

Merge pull request nf-core#648 from nf-core/dev
d4straub
authored

Commits on Nov 13, 2023

Merge pull request nf-core#660 from nf-core/dev
d4straub
authored

Commits on Nov 28, 2023

Add params.qiime_ref_tax_custom in preparation of allowing custom qiime database.
Matthew Marshall
committed
Implementation of logic to handle a custom qiime2 reference database stored in either a directory or a tarball.
Matthew Marshall
committed
Some params checking logic.
Matthew Marshall
committed
Loose . lying around.
Matthew Marshall
committed
Only perform collect if going to FORMAT_TAXONOMY_QIIME.
Matthew Marshall
committed
Set into new channel when branching on ch_qiime_ref_taxonomy.£
Matthew Marshall
committed
Try to unpack the database dir into component files using a module.
Matthew Marshall
committed
Remove map wrapping the combine.
Matthew Marshall
committed
Remove unpack in favour of map and filter.
Matthew Marshall
committed
Glob results in list in all circumstances, check length instead.
Matthew Marshall
committed
Merge remote-tracking branch 'upstream/dev' into qiime2_custom_db
Matthew Marshall
committed
Update CHANGELOG.md.
Matthew Marshall
committed

Commits on Nov 29, 2023

Update error message when passing both one of --qiime_ref_taxonomy or --qiime_ref_tax_custom and --classifier.
Matthew Marshall
committed
Update CHANGELOG.md with pull request number.

Matthew
and
d4straub
authored
Add support for specifying two (possibly gzipped) files as --qiime_ref_tax_custom.
Matthew Marshall
committed
Only support providing two files separated by a comma.
Matthew Marshall
committed
Fix split returns a String[] and we actually need an ArrayList.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Move ch_ref_database set into correct scope.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Try using map to work through list of files.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Can't call processes from inside maps.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Fix outfile definition in GZIP_DECOMPRESS.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Fix outfile definition in GZIP_DECOMPRESS.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Add some comments.
Matthew Marshall
committed
Add an early check that two paths are provided when providing a comma-separated list.
Matthew Marshall
committed
Make sure downstream is aware of new means of pointing to a qiime ref db.
Matthew Marshall
committed

Commits on Dec 1, 2023

Improve error message clarity for ill-formed file.

Matthew
and
d4straub
authored
Fix typo in error on --qiime_ref_paths form.
Matthew Marshall
committed
Remove unneeded collect from FORMAT_TAXONOMY_QIIME invocation.
Matthew Marshall
committed
Improve version tracking in PREPTAX.
Matthew Marshall
committed
Add qiime_ref_tax_custom to testing in reftaxcustom nf-test.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed

Commits on Dec 7, 2023

Don't skip qiime while testing.
Matthew Marshall
committed
Add a skip option for just downstream qiime analysis, but still perform qiime taxonomic classification.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of gitlab.stfc.ac.uk:omics/open-source-background-assets/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Skip qiime downstream in reftaxcustom.
Matthew Marshall
committed
Fix path for testing tarball passed to --qiime_ref_tax_custom.
Matthew Marshall
committed
Add snapshot of files coming from qiime2 taxonomy.
Matthew Marshall
committed
Work towards a qiime_ref_tax_custom specific test.
Matthew Marshall
committed
Skip dada tax.
Matthew Marshall
committed
Sequence then taxonomy file for file pair to --qiime_ref_tax_custom.
Matthew Marshall
committed
Clarify in help text of --qiime_ref_tax_custom the ordering of a file pair.
Matthew Marshall
committed
Update snapshots to include qiime2 in both correctly and add assertions for qiime2.
Matthew Marshall
committed
Make ordering of sequence and taxonomy files deterministic in case of file pair.
Matthew Marshall
committed
Fix filtering in file pair case.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq into qiime2_custom_db
Matthew Marshall
committed
Fix version mixing in --qiime_ref_taxonomy case.
Matthew Marshall
committed
Update software version expectations for tests that no longer run QIIME_PREPTAX.
Matthew Marshall
committed
Remove assertions on dada2 tax and phyloseq files existing in test_qiimecustom.
Matthew Marshall
committed
Looks like qiime2 tax alignment is non-deterministic, just verify the files it emits are emitted.
Matthew Marshall
committed

Commits on Dec 8, 2023

Make --skip_qiime_downstream help text clearer.

Matthew
and
d4straub
authored
Remove assertion on qiime phyloseq file no longer produced.
Matthew Marshall
committed
Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq into qiime2_custom_db
Matthew Marshall
committed

Commits on Dec 12, 2023

Merge branch 'dev' into qiime2_custom_db
d4straub
authored

Commits on Dec 19, 2023

Fix reporting
d4straub
committed