Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Release 2.8.0 #690

Merged
merged 141 commits into from
Jan 15, 2024
Merged

Release 2.8.0 #690

merged 141 commits into from
Jan 15, 2024

Commits on Nov 13, 2023

  1. bump version to 2.8.0dev

    @d4straub
    d4straub committed Nov 13, 2023
    Configuration menu
    Copy the full SHA
    3b50902 View commit details
    Browse the repository at this point in the history

  2. update changelog

    @d4straub
    d4straub committed Nov 13, 2023
    Configuration menu
    Copy the full SHA
    77bb7ec View commit details
    Browse the repository at this point in the history

  3. fix indentation

    @d4straub
    d4straub committed Nov 13, 2023
    Configuration menu
    Copy the full SHA
    2992fb7 View commit details
    Browse the repository at this point in the history

Commits on Nov 14, 2023

  1. Merge pull request #661 from d4straub/bump-version-2.7.1-to-2.8.0dev 

    Bump version 2.7.1 to 2.8.0dev
    @d4straub
    d4straub authored Nov 14, 2023
    Configuration menu
    Copy the full SHA
    1067c7c View commit details
    Browse the repository at this point in the history

Commits on Nov 28, 2023

  1. Add params.qiime_ref_tax_custom in preparation of allowing custom qii… 

    …me database.
    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    d86c569 View commit details
    Browse the repository at this point in the history

  2. Implementation of logic to handle a custom qiime2 reference database … 

    …stored in either a directory or a tarball.
    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    439097c View commit details
    Browse the repository at this point in the history

  3. Add greengenes2 2022.10 to qiime ref databases.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    d924110 View commit details
    Browse the repository at this point in the history

  4. Add greengenes2022 to acceptable qiime_ref_taxonomy values.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    1082841 View commit details
    Browse the repository at this point in the history

  5. gzip does not operate on symbolic links unless forced or, as now, tol… 

    …d to emit result to stdout.
    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    4612cd1 View commit details
    Browse the repository at this point in the history

  6. Some params checking logic.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    14c89b9 View commit details
    Browse the repository at this point in the history

  7. Loose . lying around.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    d214ec0 View commit details
    Browse the repository at this point in the history

  8. Only perform collect if going to FORMAT_TAXONOMY_QIIME.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    9346d7a View commit details
    Browse the repository at this point in the history

  9. Set into new channel when branching on ch_qiime_ref_taxonomy.£

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    ef053b1 View commit details
    Browse the repository at this point in the history

  10. Try to unpack the database dir into component files using a module.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    a48a09f View commit details
    Browse the repository at this point in the history

  11. Remove map wrapping the combine.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    a9971b6 View commit details
    Browse the repository at this point in the history

  12. Remove unpack in favour of map and filter.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    aac51bd View commit details
    Browse the repository at this point in the history

  13. Glob results in list in all circumstances, check length instead.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    1b2825e View commit details
    Browse the repository at this point in the history

  14. Update usage.md.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    c230c22 View commit details
    Browse the repository at this point in the history

  15. Merge remote-tracking branch 'upstream/dev' into greengenes_2022

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    4e32672 View commit details
    Browse the repository at this point in the history

  16. Update CHANGELOG.md.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    1dd0d8e View commit details
    Browse the repository at this point in the history

  17. Add pull request link to changelog.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    850a603 View commit details
    Browse the repository at this point in the history

  18. Merge remote-tracking branch 'upstream/dev' into qiime2_custom_db

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    a903fbe View commit details
    Browse the repository at this point in the history

  19. Update CHANGELOG.md.

    Matthew Marshall committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    a4219a0 View commit details
    Browse the repository at this point in the history

Commits on Nov 29, 2023

  1. Update error message when passing both one of --qiime_ref_taxonomy or… 

    … --qiime_ref_tax_custom and --classifier.
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    0ccf6e6 View commit details
    Browse the repository at this point in the history

  2. Update CHANGELOG.md with pull request number. 

    Co-authored-by: Daniel Straub <[email protected]>
    @d4straub
    Matthew and d4straub authored Nov 29, 2023
    Configuration menu
    Copy the full SHA
    590f415 View commit details
    Browse the repository at this point in the history

  3. Add support for specifying two (possibly gzipped) files as --qiime_re… 

    …f_tax_custom.
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    f5d80f5 View commit details
    Browse the repository at this point in the history

  4. Only support providing two files separated by a comma.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    7016682 View commit details
    Browse the repository at this point in the history

  5. Fix split returns a String[] and we actually need an ArrayList.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    79cbfe8 View commit details
    Browse the repository at this point in the history

  6. 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
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    03881b2 View commit details
    Browse the repository at this point in the history

  7. Move ch_ref_database set into correct scope.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    6d767bc View commit details
    Browse the repository at this point in the history

  8. Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op… 

    …en-source-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    af1674b View commit details
    Browse the repository at this point in the history

  9. Try using map to work through list of files.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    f76b49b View commit details
    Browse the repository at this point in the history

  10. Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op… 

    …en-source-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    31a310d View commit details
    Browse the repository at this point in the history

  11. Can't call processes from inside maps.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    0890a0e View commit details
    Browse the repository at this point in the history

  12. Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op… 

    …en-source-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    b6d0c2a View commit details
    Browse the repository at this point in the history

  13. Fix outfile definition in GZIP_DECOMPRESS.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    7276a8d View commit details
    Browse the repository at this point in the history

  14. Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op… 

    …en-source-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    a021bc5 View commit details
    Browse the repository at this point in the history

  15. Fix outfile definition in GZIP_DECOMPRESS.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    f0a8715 View commit details
    Browse the repository at this point in the history

  16. Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op… 

    …en-source-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    cfc5179 View commit details
    Browse the repository at this point in the history

  17. Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in… 

    …to qiime2_custom_db
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    8ad82f2 View commit details
    Browse the repository at this point in the history

  18. Add some comments.

    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    56f241b View commit details
    Browse the repository at this point in the history

  19. Add an early check that two paths are provided when providing a comma… 

    …-separated list.
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    7907df5 View commit details
    Browse the repository at this point in the history

  20. Make sure downstream is aware of new means of pointing to a qiime ref… 

    … db.
    Matthew Marshall committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    1d6ce32 View commit details
    Browse the repository at this point in the history

Commits on Dec 1, 2023

  1. Improve error message clarity for ill-formed file. 

    Co-authored-by: Daniel Straub <[email protected]>
    @d4straub
    Matthew and d4straub authored Dec 1, 2023
    Configuration menu
    Copy the full SHA
    913d284 View commit details
    Browse the repository at this point in the history

  2. Fix typo in error on --qiime_ref_paths form.

    Matthew Marshall committed Dec 1, 2023
    Configuration menu
    Copy the full SHA
    330bf43 View commit details
    Browse the repository at this point in the history

  3. Remove unneeded collect from FORMAT_TAXONOMY_QIIME invocation.

    Matthew Marshall committed Dec 1, 2023
    Configuration menu
    Copy the full SHA
    b8c595c View commit details
    Browse the repository at this point in the history

  4. Improve version tracking in PREPTAX.

    Matthew Marshall committed Dec 1, 2023
    Configuration menu
    Copy the full SHA
    3e05fe5 View commit details
    Browse the repository at this point in the history

  5. Add qiime_ref_tax_custom to testing in reftaxcustom nf-test.

    Matthew Marshall committed Dec 1, 2023
    Configuration menu
    Copy the full SHA
    b012aeb View commit details
    Browse the repository at this point in the history

  6. Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op… 

    …en-source-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Dec 1, 2023
    Configuration menu
    Copy the full SHA
    c5f0188 View commit details
    Browse the repository at this point in the history

Commits on Dec 5, 2023

  1. Patch summary_report as it expects qiime_ref_taxonomy is set even whe… 

    …n it can be null due to classifier being passed.
    Matthew Marshall committed Dec 5, 2023
    Configuration menu
    Copy the full SHA
    7ce4fa8 View commit details
    Browse the repository at this point in the history

Commits on Dec 6, 2023

  1. update output docs for collapsed abundance tables

    @danclaytondev
    danclaytondev committed Dec 6, 2023
    Configuration menu
    Copy the full SHA
    d83deb0 View commit details
    Browse the repository at this point in the history

Commits on Dec 7, 2023

  1. update changelog

    @danclaytondev
    danclaytondev committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    d8ea1f0 View commit details
    Browse the repository at this point in the history

  2. run prettier

    @danclaytondev
    danclaytondev committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    feacdd5 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #672 from danclaytondev/dev 

    Update output docs for collapsed abundance tables
    @danclaytondev
    danclaytondev authored Dec 7, 2023
    Configuration menu
    Copy the full SHA
    4e10651 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'dev' into bugfix/summary_report

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    4ca5f66 View commit details
    Browse the repository at this point in the history

  5. Update changelog.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    a8ec74a View commit details
    Browse the repository at this point in the history

  6. Don't skip qiime while testing.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    ba71667 View commit details
    Browse the repository at this point in the history

  7. Add a skip option for just downstream qiime analysis, but still perfo… 

    …rm qiime taxonomic classification.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    1360415 View commit details
    Browse the repository at this point in the history

  8. Merge branch 'qiime2_custom_db' of gitlab.stfc.ac.uk:omics/open-sourc… 

    …e-background-assets/ampliseq into qiime2_custom_db
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    8a9a0a2 View commit details
    Browse the repository at this point in the history

  9. Skip qiime downstream in reftaxcustom.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    f4f5cda View commit details
    Browse the repository at this point in the history

  10. Fix path for testing tarball passed to --qiime_ref_tax_custom.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    549c166 View commit details
    Browse the repository at this point in the history

  11. Add snapshot of files coming from qiime2 taxonomy.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    8516534 View commit details
    Browse the repository at this point in the history

  12. Work towards a qiime_ref_tax_custom specific test.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    745cab7 View commit details
    Browse the repository at this point in the history

  13. Skip dada tax.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    a1dfb5b View commit details
    Browse the repository at this point in the history

  14. Sequence then taxonomy file for file pair to --qiime_ref_tax_custom.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    51dc97e View commit details
    Browse the repository at this point in the history

  15. Clarify in help text of --qiime_ref_tax_custom the ordering of a file… 

    … pair.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    a33f17f View commit details
    Browse the repository at this point in the history

  16. Update snapshots to include qiime2 in both correctly and add assertio… 

    …ns for qiime2.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    8f57fae View commit details
    Browse the repository at this point in the history

  17. Make ordering of sequence and taxonomy files deterministic in case of… 

    … file pair.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    74e05b2 View commit details
    Browse the repository at this point in the history

  18. Fix filtering in file pair case.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    b65df44 View commit details
    Browse the repository at this point in the history

  19. Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in… 

    …to qiime2_custom_db
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    93e174e View commit details
    Browse the repository at this point in the history

  20. Fix version mixing in --qiime_ref_taxonomy case.

    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    45bee71 View commit details
    Browse the repository at this point in the history

  21. Update software version expectations for tests that no longer run QII… 

    …ME_PREPTAX.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    3c9eaf1 View commit details
    Browse the repository at this point in the history

  22. Remove assertions on dada2 tax and phyloseq files existing in test_qi… 

    …imecustom.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    07f4407 View commit details
    Browse the repository at this point in the history

  23. Looks like qiime2 tax alignment is non-deterministic, just verify the… 

    … files it emits are emitted.
    Matthew Marshall committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    1c129e5 View commit details
    Browse the repository at this point in the history

Commits on Dec 8, 2023

  1. Update CHANGELOG.md 

    Co-authored-by: Daniel Straub <[email protected]>
    @d4straub
    Matthew and d4straub authored Dec 8, 2023
    Configuration menu
    Copy the full SHA
    04af154 View commit details
    Browse the repository at this point in the history

  2. Make --skip_qiime_downstream help text clearer. 

    Co-authored-by: Daniel Straub <[email protected]>
    @d4straub
    Matthew and d4straub authored Dec 8, 2023
    Configuration menu
    Copy the full SHA
    2ace595 View commit details
    Browse the repository at this point in the history

  3. Remove assertion on qiime phyloseq file no longer produced.

    Matthew Marshall committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    4464c38 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in… 

    …to qiime2_custom_db
    Matthew Marshall committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    1fb5089 View commit details
    Browse the repository at this point in the history

Commits on Dec 11, 2023

  1. Move midori to get dbs in alphabetical order

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    f1a8685 View commit details
    Browse the repository at this point in the history

  2. Sort dbs in alphabetical order in schema

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    54debbf View commit details
    Browse the repository at this point in the history

  3. Spelling mistake

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    fac3d73 View commit details
    Browse the repository at this point in the history

  4. Add PhytoRef taxonomy database for chloroplast 16S

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    f61d945 View commit details
    Browse the repository at this point in the history

  5. Update CHANGELOG.md

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    58b0f72 View commit details
    Browse the repository at this point in the history

  6. Add Zehr lab nifH database

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    836bb45 View commit details
    Browse the repository at this point in the history

  7. CHANGELOG

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    e4a09ce View commit details
    Browse the repository at this point in the history

  8. Fix formatting mistake

    @erikrikarddaniel
    erikrikarddaniel committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    02a2529 View commit details
    Browse the repository at this point in the history

Commits on Dec 12, 2023

  1. Change unknown to unnversioned for PhytoRef

    @erikrikarddaniel
    erikrikarddaniel committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    09ae4b7 View commit details
    Browse the repository at this point in the history

  2. fix phyloseq

    @d4straub
    d4straub committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    9a64639 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #675 from erikrikarddaniel/add-zehr-nifh 

    Add Zehr nifH database
    @erikrikarddaniel
    erikrikarddaniel authored Dec 12, 2023
    Configuration menu
    Copy the full SHA
    a1ad717 View commit details
    Browse the repository at this point in the history

  4. use .collect() to avoid warning and adjust tests

    @d4straub
    d4straub committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    c3977cb View commit details
    Browse the repository at this point in the history

  5. combine channels instead of using .collect()

    @d4straub
    d4straub committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    a32b582 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #673 from MatthewJM96/bugfix/summary_report 

    Fix qiime2 taxonomy part of summary report using unavailable information.
    @d4straub
    d4straub authored Dec 12, 2023
    Configuration menu
    Copy the full SHA
    0b29755 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'dev' into fix_phyloseq_input

    @d4straub
    d4straub authored Dec 12, 2023
    Configuration menu
    Copy the full SHA
    99b1db6 View commit details
    Browse the repository at this point in the history

  8. Merge pull request #676 from d4straub/fix_phyloseq_input 

    Fix phyloseq input
    @d4straub
    d4straub authored Dec 12, 2023
    Configuration menu
    Copy the full SHA
    746c524 View commit details
    Browse the repository at this point in the history

  9. Merge branch 'dev' into qiime2_custom_db

    @d4straub
    d4straub authored Dec 12, 2023
    Configuration menu
    Copy the full SHA
    0287ba9 View commit details
    Browse the repository at this point in the history

  10. Add cut_its to SBDI export

    @jtangrot
    jtangrot committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    9550aec View commit details
    Browse the repository at this point in the history

  11. Update CHANGELOG

    @jtangrot
    jtangrot committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    cb51739 View commit details
    Browse the repository at this point in the history

  12. Merge branch 'dev' of https://github.com/nf-core/ampliseq into update… 

    …_sbdiexport
    @jtangrot
    jtangrot committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    40b13b9 View commit details
    Browse the repository at this point in the history

  13. Update CHANGELOG

    @jtangrot
    jtangrot committed Dec 12, 2023
    Configuration menu
    Copy the full SHA
    667189c View commit details
    Browse the repository at this point in the history

Commits on Dec 13, 2023

  1. Merge pull request #677 from jtangrot/update_sbdiexport 

    Update sbdiexport
    @jtangrot
    jtangrot authored Dec 13, 2023
    Configuration menu
    Copy the full SHA
    481f3f8 View commit details
    Browse the repository at this point in the history

Commits on Dec 19, 2023

  1. Fix reporting

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    6b71e4d View commit details
    Browse the repository at this point in the history

  2. Merge pull request #667 from MatthewJM96/qiime2_custom_db 

    Added QIIME2 custom reference database support.
    @d4straub
    d4straub authored Dec 19, 2023
    Configuration menu
    Copy the full SHA
    a86f9c7 View commit details
    Browse the repository at this point in the history

  3. Prevent masking low complexity regions by VSEARCH

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    67da933 View commit details
    Browse the repository at this point in the history

  4. fix error message for --input_folder

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    a1992a4 View commit details
    Browse the repository at this point in the history

  5. Fix hyphens

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    55116e0 View commit details
    Browse the repository at this point in the history

  6. only report input folder when it is created

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    51ee751 View commit details
    Browse the repository at this point in the history

  7. report correct cutadapt percentages for all possible number ranges

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    f572faf View commit details
    Browse the repository at this point in the history

  8. update changelog

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    13a6e5e View commit details
    Browse the repository at this point in the history

  9. Merge pull request #679 from d4straub/fix-vsearch-cluster 

    Prevent masking low complexity regions by VSEARCH
    @d4straub
    d4straub authored Dec 19, 2023
    Configuration menu
    Copy the full SHA
    de53107 View commit details
    Browse the repository at this point in the history

  10. Merge branch 'dev' into fix-report

    @d4straub
    d4straub authored Dec 19, 2023
    Configuration menu
    Copy the full SHA
    f1ae7cb View commit details
    Browse the repository at this point in the history

  11. Merge pull request #680 from d4straub/fix-report 

    Improved pipeline summary report & error message
    @d4straub
    d4straub authored Dec 19, 2023
    Configuration menu
    Copy the full SHA
    709dea9 View commit details
    Browse the repository at this point in the history

  12. add --dada_addspecies_allowmultiple and --dada_taxonomy_rc

    @d4straub
    d4straub committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    d0786b7 View commit details
    Browse the repository at this point in the history

  13. Template update for nf-core/tools version 2.11

    @nf-core-bot
    nf-core-bot committed Dec 19, 2023
    Configuration menu
    Copy the full SHA
    2edaa5a View commit details
    Browse the repository at this point in the history

Commits on Dec 20, 2023

  1. Merge pull request #681 from d4straub/add-dada_addspecies_allowmultip… 

    …le-dada_taxonomy_rc

Add two parameters for taxonomic classification with DADA2
    @d4straub
    d4straub authored Dec 20, 2023
    Configuration menu
    Copy the full SHA
    71ee3c1 View commit details
    Browse the repository at this point in the history

  2. merging-template-updates-2-11

    @d4straub
    d4straub committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    df8ce82 View commit details
    Browse the repository at this point in the history

  3. update README.md to github style syntax

    @d4straub
    d4straub committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    b8648b2 View commit details
    Browse the repository at this point in the history

  4. update CHANGELOG.md

    @d4straub
    d4straub committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    9ebe892 View commit details
    Browse the repository at this point in the history

  5. adjust some assertions in .nf.test.snap

    @d4straub
    d4straub committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    cbe6bf9 View commit details
    Browse the repository at this point in the history

  6. update docker runOptions

    @d4straub
    d4straub committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    1e14c0e View commit details
    Browse the repository at this point in the history

  7. adjust pplace.nf.test.snap

    @d4straub
    d4straub committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    9742624 View commit details
    Browse the repository at this point in the history

  8. Merge pull request #683 from d4straub/merging-template-updates-2-11 

    Merging template updates 2.11
    @d4straub
    d4straub authored Dec 20, 2023
    Configuration menu
    Copy the full SHA
    4b616ed View commit details
    Browse the repository at this point in the history

  9. Template update for nf-core/tools version 2.11.1

    @nf-core-bot
    nf-core-bot committed Dec 20, 2023
    Configuration menu
    Copy the full SHA
    127b88a View commit details
    Browse the repository at this point in the history

Commits on Dec 21, 2023

  1. Merge pull request #684 from nf-core/nf-core-template-merge-2.11.1 

    Important! Template update for nf-core/tools v2.11.1
    @d4straub
    d4straub authored Dec 21, 2023
    Configuration menu
    Copy the full SHA
    eadcd30 View commit details
    Browse the repository at this point in the history

  2. merge dev

    @d4straub
    d4straub committed Dec 21, 2023
    Configuration menu
    Copy the full SHA
    975e6d4 View commit details
    Browse the repository at this point in the history

  3. Apply suggestions from code review

    @d4straub
    d4straub authored Dec 21, 2023
    Configuration menu
    Copy the full SHA
    815e62b View commit details
    Browse the repository at this point in the history

Commits on Jan 11, 2024

  1. activate multi-cpu use in QIIME2_EXTRACT

    @d4straub
    d4straub committed Jan 11, 2024
    Configuration menu
    Copy the full SHA
    70b2e01 View commit details
    Browse the repository at this point in the history

Commits on Jan 12, 2024

  1. Merge pull request #666 from MatthewJM96/greengenes_2022 

    Greengenes2 2022.10 Support
    @d4straub
    d4straub authored Jan 12, 2024
    Configuration menu
    Copy the full SHA
    1798c4a View commit details
    Browse the repository at this point in the history

  2. fix conda package in FILTER_SSU

    @d4straub
    d4straub committed Jan 12, 2024
    Configuration menu
    Copy the full SHA
    54e3d60 View commit details
    Browse the repository at this point in the history

  3. update docs

    @d4straub
    d4straub committed Jan 12, 2024
    Configuration menu
    Copy the full SHA
    06dcda7 View commit details
    Browse the repository at this point in the history

  4. Merge pull request #687 from d4straub/fix-FILTER_SSU-conda 

    fix conda package in FILTER_SSU
    @d4straub
    d4straub authored Jan 12, 2024
    Configuration menu
    Copy the full SHA
    591ac20 View commit details
    Browse the repository at this point in the history

  5. Apply suggestions from code review 

    Co-authored-by: Till E. <[email protected]>
    @d4straub @tillenglert
    d4straub and tillenglert authored Jan 12, 2024
    Configuration menu
    Copy the full SHA
    9dbb353 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #688 from d4straub/update-docs-tax-databases 

    Update docs, citations and usage with new taxonomic reference databases
    @d4straub
    d4straub authored Jan 12, 2024
    Configuration menu
    Copy the full SHA
    c92e172 View commit details
    Browse the repository at this point in the history

  7. bump version to 2.8.0

    @d4straub
    d4straub committed Jan 12, 2024
    Configuration menu
    Copy the full SHA
    08cb7f0 View commit details
    Browse the repository at this point in the history

  8. fix prettier

    @d4straub
    d4straub committed Jan 12, 2024
    Configuration menu
    Copy the full SHA
    24ab709 View commit details
    Browse the repository at this point in the history

  9. Merge pull request #689 from d4straub/bump-version-2.8.0 

    bump version to 2.8.0
    @d4straub
    d4straub authored Jan 12, 2024
    Configuration menu
    Copy the full SHA
    7ebd565 View commit details
    Browse the repository at this point in the history

Commits on Jan 15, 2024

  1. update parameter help

    @d4straub
    d4straub committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    0be678e View commit details
    Browse the repository at this point in the history

  2. update qiime_ref_tax_custom help text

    @d4straub
    d4straub committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    678ce1a View commit details
    Browse the repository at this point in the history

  3. change qiime_ref_tax_custom test files to nf-core

    @d4straub
    d4straub committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    5ad866f View commit details
    Browse the repository at this point in the history

  4. replace local gzip with nf-core module pigz/uncompress

    @d4straub
    d4straub committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    4694510 View commit details
    Browse the repository at this point in the history

  5. fix typo

    @d4straub
    d4straub committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    08353dd View commit details
    Browse the repository at this point in the history

  6. Merge pull request #691 from d4straub/reviewer-comments-2-8-0 

    Reviewer comments 2.8.0
    @d4straub
    d4straub authored Jan 15, 2024
    Configuration menu
    Copy the full SHA
    2c67a45 View commit details
    Browse the repository at this point in the history