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Release 2.8.0 #690

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merged 141 commits into from
Jan 15, 2024
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3b50902
bump version to 2.8.0dev
d4straub Nov 13, 2023
77bb7ec
update changelog
d4straub Nov 13, 2023
2992fb7
fix indentation
d4straub Nov 13, 2023
1067c7c
Merge pull request #661 from d4straub/bump-version-2.7.1-to-2.8.0dev
d4straub Nov 14, 2023
d86c569
Add params.qiime_ref_tax_custom in preparation of allowing custom qii…
Nov 28, 2023
439097c
Implementation of logic to handle a custom qiime2 reference database …
Nov 28, 2023
d924110
Add greengenes2 2022.10 to qiime ref databases.
Nov 28, 2023
1082841
Add greengenes2022 to acceptable qiime_ref_taxonomy values.
Nov 28, 2023
4612cd1
gzip does not operate on symbolic links unless forced or, as now, tol…
Nov 28, 2023
14c89b9
Some params checking logic.
Nov 28, 2023
d214ec0
Loose . lying around.
Nov 28, 2023
9346d7a
Only perform collect if going to FORMAT_TAXONOMY_QIIME.
Nov 28, 2023
ef053b1
Set into new channel when branching on ch_qiime_ref_taxonomy.£
Nov 28, 2023
a48a09f
Try to unpack the database dir into component files using a module.
Nov 28, 2023
a9971b6
Remove map wrapping the combine.
Nov 28, 2023
aac51bd
Remove unpack in favour of map and filter.
Nov 28, 2023
1b2825e
Glob results in list in all circumstances, check length instead.
Nov 28, 2023
c230c22
Update usage.md.
Nov 28, 2023
4e32672
Merge remote-tracking branch 'upstream/dev' into greengenes_2022
Nov 28, 2023
1dd0d8e
Update CHANGELOG.md.
Nov 28, 2023
850a603
Add pull request link to changelog.
Nov 28, 2023
a903fbe
Merge remote-tracking branch 'upstream/dev' into qiime2_custom_db
Nov 28, 2023
a4219a0
Update CHANGELOG.md.
Nov 28, 2023
0ccf6e6
Update error message when passing both one of --qiime_ref_taxonomy or…
Nov 29, 2023
590f415
Update CHANGELOG.md with pull request number.
Nov 29, 2023
f5d80f5
Add support for specifying two (possibly gzipped) files as --qiime_re…
Nov 29, 2023
7016682
Only support providing two files separated by a comma.
Nov 29, 2023
79cbfe8
Fix split returns a String[] and we actually need an ArrayList.
Nov 29, 2023
03881b2
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Nov 29, 2023
6d767bc
Move ch_ref_database set into correct scope.
Nov 29, 2023
af1674b
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Nov 29, 2023
f76b49b
Try using map to work through list of files.
Nov 29, 2023
31a310d
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Nov 29, 2023
0890a0e
Can't call processes from inside maps.
Nov 29, 2023
b6d0c2a
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Nov 29, 2023
7276a8d
Fix outfile definition in GZIP_DECOMPRESS.
Nov 29, 2023
a021bc5
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Nov 29, 2023
f0a8715
Fix outfile definition in GZIP_DECOMPRESS.
Nov 29, 2023
cfc5179
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Nov 29, 2023
8ad82f2
Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in…
Nov 29, 2023
56f241b
Add some comments.
Nov 29, 2023
7907df5
Add an early check that two paths are provided when providing a comma…
Nov 29, 2023
1d6ce32
Make sure downstream is aware of new means of pointing to a qiime ref…
Nov 29, 2023
913d284
Improve error message clarity for ill-formed file.
Dec 1, 2023
330bf43
Fix typo in error on --qiime_ref_paths form.
Dec 1, 2023
b8c595c
Remove unneeded collect from FORMAT_TAXONOMY_QIIME invocation.
Dec 1, 2023
3e05fe5
Improve version tracking in PREPTAX.
Dec 1, 2023
b012aeb
Add qiime_ref_tax_custom to testing in reftaxcustom nf-test.
Dec 1, 2023
c5f0188
Merge branch 'qiime2_custom_db' of https://gitlab.stfc.ac.uk/omics/op…
Dec 1, 2023
7ce4fa8
Patch summary_report as it expects qiime_ref_taxonomy is set even whe…
Dec 5, 2023
d83deb0
update output docs for collapsed abundance tables
danclaytondev Dec 6, 2023
d8ea1f0
update changelog
danclaytondev Dec 7, 2023
feacdd5
run prettier
danclaytondev Dec 7, 2023
4e10651
Merge pull request #672 from danclaytondev/dev
danclaytondev Dec 7, 2023
4ca5f66
Merge branch 'dev' into bugfix/summary_report
Dec 7, 2023
a8ec74a
Update changelog.
Dec 7, 2023
ba71667
Don't skip qiime while testing.
Dec 7, 2023
1360415
Add a skip option for just downstream qiime analysis, but still perfo…
Dec 7, 2023
8a9a0a2
Merge branch 'qiime2_custom_db' of gitlab.stfc.ac.uk:omics/open-sourc…
Dec 7, 2023
f4f5cda
Skip qiime downstream in reftaxcustom.
Dec 7, 2023
549c166
Fix path for testing tarball passed to --qiime_ref_tax_custom.
Dec 7, 2023
8516534
Add snapshot of files coming from qiime2 taxonomy.
Dec 7, 2023
745cab7
Work towards a qiime_ref_tax_custom specific test.
Dec 7, 2023
a1dfb5b
Skip dada tax.
Dec 7, 2023
51dc97e
Sequence then taxonomy file for file pair to --qiime_ref_tax_custom.
Dec 7, 2023
a33f17f
Clarify in help text of --qiime_ref_tax_custom the ordering of a file…
Dec 7, 2023
8f57fae
Update snapshots to include qiime2 in both correctly and add assertio…
Dec 7, 2023
74e05b2
Make ordering of sequence and taxonomy files deterministic in case of…
Dec 7, 2023
b65df44
Fix filtering in file pair case.
Dec 7, 2023
93e174e
Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in…
Dec 7, 2023
45bee71
Fix version mixing in --qiime_ref_taxonomy case.
Dec 7, 2023
3c9eaf1
Update software version expectations for tests that no longer run QII…
Dec 7, 2023
07f4407
Remove assertions on dada2 tax and phyloseq files existing in test_qi…
Dec 7, 2023
1c129e5
Looks like qiime2 tax alignment is non-deterministic, just verify the…
Dec 7, 2023
04af154
Update CHANGELOG.md
Dec 8, 2023
2ace595
Make --skip_qiime_downstream help text clearer.
Dec 8, 2023
4464c38
Remove assertion on qiime phyloseq file no longer produced.
Dec 8, 2023
1fb5089
Merge branch 'qiime2_custom_db' of github.com:MatthewJM96/ampliseq in…
Dec 8, 2023
f1a8685
Move midori to get dbs in alphabetical order
erikrikarddaniel Dec 11, 2023
54debbf
Sort dbs in alphabetical order in schema
erikrikarddaniel Dec 11, 2023
fac3d73
Spelling mistake
erikrikarddaniel Dec 11, 2023
f61d945
Add PhytoRef taxonomy database for chloroplast 16S
erikrikarddaniel Dec 11, 2023
58b0f72
Update CHANGELOG.md
erikrikarddaniel Dec 11, 2023
836bb45
Add Zehr lab nifH database
erikrikarddaniel Dec 11, 2023
e4a09ce
CHANGELOG
erikrikarddaniel Dec 11, 2023
02a2529
Fix formatting mistake
erikrikarddaniel Dec 11, 2023
09ae4b7
Change unknown to unnversioned for PhytoRef
erikrikarddaniel Dec 12, 2023
9a64639
fix phyloseq
d4straub Dec 12, 2023
a1ad717
Merge pull request #675 from erikrikarddaniel/add-zehr-nifh
erikrikarddaniel Dec 12, 2023
c3977cb
use .collect() to avoid warning and adjust tests
d4straub Dec 12, 2023
a32b582
combine channels instead of using .collect()
d4straub Dec 12, 2023
0b29755
Merge pull request #673 from MatthewJM96/bugfix/summary_report
d4straub Dec 12, 2023
99b1db6
Merge branch 'dev' into fix_phyloseq_input
d4straub Dec 12, 2023
746c524
Merge pull request #676 from d4straub/fix_phyloseq_input
d4straub Dec 12, 2023
0287ba9
Merge branch 'dev' into qiime2_custom_db
d4straub Dec 12, 2023
9550aec
Add cut_its to SBDI export
jtangrot Dec 12, 2023
cb51739
Update CHANGELOG
jtangrot Dec 12, 2023
40b13b9
Merge branch 'dev' of https://github.com/nf-core/ampliseq into update…
jtangrot Dec 12, 2023
667189c
Update CHANGELOG
jtangrot Dec 12, 2023
481f3f8
Merge pull request #677 from jtangrot/update_sbdiexport
jtangrot Dec 13, 2023
6b71e4d
Fix reporting
d4straub Dec 19, 2023
a86f9c7
Merge pull request #667 from MatthewJM96/qiime2_custom_db
d4straub Dec 19, 2023
67da933
Prevent masking low complexity regions by VSEARCH
d4straub Dec 19, 2023
a1992a4
fix error message for --input_folder
d4straub Dec 19, 2023
55116e0
Fix hyphens
d4straub Dec 19, 2023
51ee751
only report input folder when it is created
d4straub Dec 19, 2023
f572faf
report correct cutadapt percentages for all possible number ranges
d4straub Dec 19, 2023
13a6e5e
update changelog
d4straub Dec 19, 2023
de53107
Merge pull request #679 from d4straub/fix-vsearch-cluster
d4straub Dec 19, 2023
f1ae7cb
Merge branch 'dev' into fix-report
d4straub Dec 19, 2023
709dea9
Merge pull request #680 from d4straub/fix-report
d4straub Dec 19, 2023
d0786b7
add --dada_addspecies_allowmultiple and --dada_taxonomy_rc
d4straub Dec 19, 2023
2edaa5a
Template update for nf-core/tools version 2.11
nf-core-bot Dec 19, 2023
71ee3c1
Merge pull request #681 from d4straub/add-dada_addspecies_allowmultip…
d4straub Dec 20, 2023
df8ce82
merging-template-updates-2-11
d4straub Dec 20, 2023
b8648b2
update README.md to github style syntax
d4straub Dec 20, 2023
9ebe892
update CHANGELOG.md
d4straub Dec 20, 2023
cbe6bf9
adjust some assertions in .nf.test.snap
d4straub Dec 20, 2023
1e14c0e
update docker runOptions
d4straub Dec 20, 2023
9742624
adjust pplace.nf.test.snap
d4straub Dec 20, 2023
4b616ed
Merge pull request #683 from d4straub/merging-template-updates-2-11
d4straub Dec 20, 2023
127b88a
Template update for nf-core/tools version 2.11.1
nf-core-bot Dec 20, 2023
eadcd30
Merge pull request #684 from nf-core/nf-core-template-merge-2.11.1
d4straub Dec 21, 2023
975e6d4
merge dev
d4straub Dec 21, 2023
815e62b
Apply suggestions from code review
d4straub Dec 21, 2023
70b2e01
activate multi-cpu use in QIIME2_EXTRACT
d4straub Jan 11, 2024
1798c4a
Merge pull request #666 from MatthewJM96/greengenes_2022
d4straub Jan 12, 2024
54e3d60
fix conda package in FILTER_SSU
d4straub Jan 12, 2024
06dcda7
update docs
d4straub Jan 12, 2024
591ac20
Merge pull request #687 from d4straub/fix-FILTER_SSU-conda
d4straub Jan 12, 2024
9dbb353
Apply suggestions from code review
d4straub Jan 12, 2024
c92e172
Merge pull request #688 from d4straub/update-docs-tax-databases
d4straub Jan 12, 2024
08cb7f0
bump version to 2.8.0
d4straub Jan 12, 2024
24ab709
fix prettier
d4straub Jan 12, 2024
7ebd565
Merge pull request #689 from d4straub/bump-version-2.8.0
d4straub Jan 12, 2024
0be678e
update parameter help
d4straub Jan 15, 2024
678ce1a
update qiime_ref_tax_custom help text
d4straub Jan 15, 2024
5ad866f
change qiime_ref_tax_custom test files to nf-core
d4straub Jan 15, 2024
4694510
replace local gzip with nf-core module pigz/uncompress
d4straub Jan 15, 2024
08353dd
fix typo
d4straub Jan 15, 2024
2c67a45
Merge pull request #691 from d4straub/reviewer-comments-2-8-0
d4straub Jan 15, 2024
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adjust pplace.nf.test.snap
d4straub committed Dec 20, 2023
commit 9742624b19082a54fd481119406785af6bc802d6
2 changes: 1 addition & 1 deletion tests/pipeline/pplace.nf.test.snap

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