[PSEUDO-PR - DO NOT MERGE] core team release review - #79

Closed

jfy133 wants to merge 353 commits into

This pull request is big! We're only showing the most recent 250 commits

Commits on Mar 23, 2026

Merge branch 'update-multiqc' into nw-dev
nickp60
committed
909c8c3
passing in stub mode
nickp60
committed
d4145e1

Commits on Mar 24, 2026

update modules
nickp60
committed
10275be

Commits on Mar 25, 2026

most tests passing
nickp60
committed
11aa244
whitespace fix
nickp60
committed
6835ef8
Merge pull request #34 from nickp60/nw-dev
nickp60
authored
c3d943f

Commits on Mar 27, 2026

test explicitly listing the container not using function
baichom1
committed
042356e
fix whitespace
baichom1
committed
ef5825d
use withName instead
baichom1
committed
a706275
adds missing paren
miraep8
committed
934b8b7
whoops
miraep8
committed
2a9709c
try with task.process not name
miraep8
committed
bda4d14
move regroup to aliases
nickp60
committed
a265ab7
fix profiling alias
nickp60
committed
6cf5b92
revert container fetching
nickp60
committed
1befee1
add dummy entry to container selection for paritail compliance with
nickp60
committed
d453892
add dummy processes to trick nextflow inspect into cooperating
nickp60
committed
664e0ea
fix weird absolute path issue
nickp60
committed
f792c49

Commits on Mar 28, 2026

disable diamond for test profile
nickp60
committed
786b91b

Commits on Mar 30, 2026

update snapshot
miraep8
committed
e28d0dc
try janky environmet file
miraep8
committed
89f04ff
pre-commit
miraep8
committed
86f4ecd
update env
miraep8
committed
9d0b4ec
fix env locally
miraep8
committed
68cc530
adds git
miraep8
committed
cfaedfd
temporarily reduce tests
miraep8
committed
33c09ce
adds docker where appropriate and manually installs fmh-funcprofiler for conda and mamba profile
miraep8
committed
667d7bf
adds conditional install to stub as well
miraep8
committed
ba18759
explicit call to python?
miraep8
committed
f0a3805
explicit call to python when not installed
miraep8
committed
e3e6eec
add python to versions as well
miraep8
committed
0ee3027
udate snapshot to include help not version for fmh-funcprofiler
miraep8
committed
db752a3

Commits on Mar 31, 2026

reset tests and also ditch the conditional install
miraep8
committed
8cbc0ea

Commits on Apr 2, 2026

Improve docs
vinisalazar
committed
7b326e0
Apply pre-commit fixes
vinisalazar
committed
7be5f94
Improve text
vinisalazar
committed
73ba613
Pre-commit again
vinisalazar
committed
2ca4781
error if fmhfunprofiler is run without container. Test skips run_fmhfunprofiler if running conda
miraep8
committed
2816fde
attempts mifaser env
miraep8
committed
92c4904
precommit and fix profile def
miraep8
committed
20a1f1d
flip sign
miraep8
committed
7ad3dbd
update mifaser version
miraep8
committed
bd4c8c9
resotre test snapshot
miraep8
committed
d23e157
temporarily turn off latest everything and update snapshots
miraep8
committed
89d95d6
actually update snapshot with correct nf version and singularity profile
miraep8
committed
fcc7160
simplify container paths
miraep8
committed
815320f

Commits on Apr 8, 2026

update mifaser to conda version - yay!
miraep8
committed
7cc16fc

Commits on Apr 9, 2026

fix eof
nickp60
committed
231528e
disable conda from ci
nickp60
committed
6d8d3bd
fix name, bump shards
nickp60
committed
9ac4648
remove yml from tests, re-enable fmhfunprofiler for tests
nickp60
committed
803cb9c
simplify regroup singularity prefix
nickp60
committed
f2feaa9
Merge pull request #38 from vinisalazar/docs
vinisalazar
authored
24178ea
fix snap
nickp60
committed
89ec4fe
Merge branch 'dev' of github.com:nf-core/funcprofiler into dev
nickp60
committed
5902136
fix .nftignore
nickp60
committed
68521d5

Commits on Apr 10, 2026

bump shards further
nickp60
committed
b362cf6
attempt to bump storage on runner
nickp60
committed
341fcd8
try smaller image
miraep8
committed
797a560
fix typo
miraep8
committed
1e72710
rollback image
miraep8
committed
75e6b99
try out small figure again
miraep8
committed
b8ecd26
new image, tried it out locally first this time :)
miraep8
committed
4e676aa
make humann3 smaller as well
miraep8
committed
a93f863
remove volume bump since it curiously increased number of failing jobs
miraep8
committed
c481794

Commits on Apr 14, 2026

mifaser: in tests, only check for file existence and name.
vinisalazar
committed
1617f95
Add non-deterministic files to .nftignore
vinisalazar
committed
a80bc72
Update snapshot
vinisalazar
committed
ede7787
Use correct extension in ignored files
vinisalazar
committed
d5a20da
Remove genefamilies from humann/main_v4 stub test
vinisalazar
committed
f8666f6
Do the same for humann_v3 test
vinisalazar
committed
ef8fe5e
Update snapshots
vinisalazar
committed
b6bb063
Increase singularity.pullTimeout
vinisalazar
committed
cc3a454
Move singularity.pullTimeout to tests/nextflow.config
vinisalazar
committed
0b69293
Add HUMAnN {sample}_reactions.tsv file to .nftignore
vinisalazar
committed
8aa5eb9
attmept 1 at getting artifact
nickp60
committed
1853aea
whitespace
nickp60
committed
d380906
make conditional
nickp60
committed
1d377d6
fix syntax
nickp60
committed
50316cc
doh
nickp60
committed
ef65a4e
list before upload attempt
nickp60
committed
11d7fa5
make artifacts uniq
nickp60
committed
d0f0b9c
typo
nickp60
committed
e3a27b6
more typo fixes
nickp60
committed
762e4af
add shard to artifact id
nickp60
committed
2d27f02
force artifacts
nickp60
committed
e49c571
made test data smaller, skip stub, override mpa container
nickp60
committed
e9e9a7d
update module-level snap
nickp60
committed
12eac7b
update renorm container to most recent, hardcoded
nickp60
committed
1766752
update snapshot to fix header after renorm bump
nickp60
committed
d48c849

Commits on Apr 16, 2026

WIP major refactor to clean up input mess
nickp60
committed
7ead87b
WIP
nickp60
committed
f63b1a0
add tests for run-merging off/on
nickp60
committed
bbff4b8
add tests for prepareInput function
nickp60
committed
0c918fa
WIP update profile subworkflow next
nickp60
committed
9bae988

Commits on Apr 17, 2026

WIP fixing db parsing structure
nickp60
committed
f9544ad
fix db parse param location
nickp60
committed
4f13fe7
unify test
nickp60
committed
b025de0
restructured all profiling
nickp60
committed
5588bd1
haven't rebuilt snapshots but pushing anyway
nickp60
committed
a529ccf
remove fmhfunprofler garbage workarounds
nickp60
committed
d3a7ece
unify tuple input for fmhfunprofiler
nickp60
committed
503597c
passing local tests
nickp60
committed
2eeeec1
remove file() from tests to prevent abs paths
nickp60
committed
4d341ee
swap out arraylist for map
nickp60
committed
3bbc90d
fix order
nickp60
committed
84416b0

Commits on Apr 18, 2026

attmpt 1 at resolve collision
nickp60
committed
1287778

Commits on Apr 20, 2026

attempt add sample mixup test
nickp60
committed
37e4fa0
attempt 2
nickp60
committed
c4316b5
fix test
nickp60
committed
6df114f
update
nickp60
committed
ac29fb7
add cleanup false to retain .command files
nickp60
committed
8747c12
hotfix removes the cleanup from nf test config
baichom1
committed
1329db9
syntax
nickp60
committed
e3d3372
Merge branch 'get-build-artifacts' of github.com:nf-core/funcprofiler into get-build-artifacts
nickp60
committed
db0b5ec
push drop retention
nickp60
committed
0b60093
untabbify
nickp60
committed
12a5ae8

Commits on Apr 21, 2026

refactor humann to separate modules :(
nickp60
committed
4d39d00
fix sort, fix import
nickp60
committed
87e0314
update
nickp60
committed
585d802
fix versions
nickp60
committed
5ab29a6
snapshot only reads not dbs, disable humann4 for tests
nickp60
committed
551b999
update snap
nickp60
committed
0cf765b
more separation
nickp60
committed
a532a7d
just reorders test input
miraep8
committed
a4c227d
adds back dbs to prepareInputs snap
miraep8
committed
da969fc
add back humannv4
nickp60
committed
967ebd6
sorts keys and input
miraep8
committed
6320c28

Commits on Apr 22, 2026

join mpa with reads before humann
nickp60
committed
a644931
Merge remote-tracking branch 'origin/minimal_change_parallel_debug' into get-build-artifacts
nickp60
committed
c1cbe94
clean up humann meta
nickp60
committed
56f0ea0
syntax, fix test input url
nickp60
committed
08237bc
syntax
nickp60
committed
bebc86f
update snapshots
nickp60
committed
da2f92c

Commits on Apr 28, 2026

Commits on Apr 29, 2026

runs nextflow lint on all nf files
miraep8
committed
e4e8b51
same issues with test and netflix version
miraep8
committed
833b2df
Merge pull request #54 from nf-core/fix_linting
miraep8
authored
37559e6

Commits on Apr 30, 2026

Mark DIAMOND and eggNOG-mapper as beta in README
Yixuan39
authored
3bbdabd

Commits on May 10, 2026

Update DIAMOND/EggNOG status and warnings
Yixuan39
committed
47625fc
Fix website issues
Yixuan39
committed
6ab44a3

Commits on May 12, 2026

fix: wrap ext.prefix ternary inside single closure
vinisalazar
committed
be25804
fix(fmhfunprofiler): fix typo, remove TODOs, fix version string
vinisalazar
committed
d1fa49d
fix(fmhfunprofiler): remove TODO comments from tests
vinisalazar
committed
ab360d1
fix(fmhfunprofiler): rewrite meta.yml with correct inputs/outputs
vinisalazar
committed
0bdc1ab
docs: rewrite output.md per nf-core conventions
vinisalazar
committed
584b2f1
docs: convert GitHub admonitions to nf-core website admonitions
vinisalazar
committed
a5a0903
chore: sync RO-Crate description from README
vinisalazar
committed
834ae70
Apply pre-commit
vinisalazar
committed
ff12832
Merge pull request #57 from Yixuan39/dev
vinisalazar
authored
8c4b3a4
Merge branch 'dev' into pr52-code-review-minor
vinisalazar
authored
ae0162f
Update snapshots
vinisalazar
committed
630bfc2
Merge pull request #59 from vinisalazar/pr52-code-review-minor
vinisalazar
authored
292e231
Resolve merge conflicts from nf-core-template-merge-4.0.2

vinisalazar
and
claude
committed
745df54
Fix Nextflow lint errors from template merge

vinisalazar
and
claude
committed
15ce257
Fix more pre-commit errors
vinisalazar
committed
d45e41f
Remove lint ignores
vinisalazar
committed
cd18e2e

Commits on May 13, 2026

Remove names of tools from error message
vinisalazar
committed
76896b2

Commits on May 15, 2026

cat/fastq: update module
vinisalazar
committed
c55af29
eggnogmapper: update module
vinisalazar
committed
e7c6004
metaphlan/metaphlan: update module
vinisalazar
committed
724a15d
rgi/bwt: update module
vinisalazar
committed
60a5615
seqkit/fq2fa: update module
vinisalazar
committed
fcb50b6
Linting modules
vinisalazar
committed
beeecbc
Add 'Install Nextflow' action
vinisalazar
committed
2e61cf0
Update nf-core config
vinisalazar
committed
662904e
Update subworkflow 'utils_nextflow_pipeline'
vinisalazar
committed
17c8094
Update subworkflow 'utils_nfcore_pipeline'
vinisalazar
committed
16f8db1
Update subworkflow 'utils_nfschema_plugin'
vinisalazar
committed
a0f59ef
fix: add missing cli_typecast arg to UTILS_NFSCHEMA_PLUGIN call
vinisalazar
committed
8b2a6c2
ci: update nf-test.yml workflow file
vinisalazar
committed
03e2145

Commits on May 22, 2026

WIP fulltest with interim paths
nickp60
committed
385a3cb

Commits on May 23, 2026

Merge branch 'dev' into dev-update-template
vinisalazar
committed
630c581
Remove names of tools from error message
vinisalazar
committed
b117aaa
Merge branch 'dev' into dev-update-template
vinisalazar
committed
374319f
Merge pull request #60 from vinisalazar/dev-update-template
vinisalazar
authored
578b0c4
Linting: fix version string
vinisalazar
committed
c385559
Install nf-core humann3 and mifaser modules
vinisalazar
committed
945efa2
Use nf-core humann3 and mifaser in profile workflow
vinisalazar
committed
d0f94f4
Remove replaced local humann3 and mifaser modules
vinisalazar
committed
b0d1f27
Linting: pin multiqc report_comment to 1.0.0
vinisalazar
committed
646f37c

Commits on Jun 12, 2026

fix snapshot; mifaser fixed in testdatasets
nickp60
committed
b0917e7

Commits on Jun 25, 2026

exclude pesky non-deterministic regroupung for test profile; add cardannotation so tests pass
nickp60
committed
4d4b8c5

Commits on Jul 2, 2026

re-enable conda support after tools were added to bioconda (#63)
nickp60
authored
df8c6f9

Commits on Jul 7, 2026

Commits on Jul 8, 2026

snapshot versions to clarify issue
nickp60
committed
fea6860
bump rgi version
nickp60
committed
d3ec186

Commits on Jul 9, 2026

attempt remove global topic tag
nickp60
committed
a2dc0ce
bump nf-test to version supporting topics
nickp60
committed
6446f24
clean up prior to lint fix
nickp60
committed
1d415f1
reinstall multiqc to fix conf issue
nickp60
committed
a72f04e
WIP cleaning up lint comments
nickp60
committed
d689a3f

Commits on Jul 13, 2026

more lint cleanups
nickp60
committed
d334781

Commits on Jul 14, 2026

temporary fix fmhfuncprofiler test
nickp60
committed
71735ed
prek
nickp60
committed
3845079
Template update for nf-core/tools version 4.0.3.dev0
nickp60
committed
1846312
attempt bump template
nickp60
committed
4cdaf37
bump sticky pull comment to 3.0.5 to avoid node 20 error
nickp60
committed
5c2be92
increase shards, add valid nf-core version
nickp60
committed
a0d2bf9

Commits on Jul 23, 2026

Commits on Jul 24, 2026

swap in module for fmhfunprofiler
nickp60
committed
ca2080d
Merge branch 'dev' of github.com:nf-core/funcprofiler into dev
nickp60
committed
e8d9f16
merge template
nickp60
committed
e47a3f3
fix rocrate
nickp60
committed
1e0dcce
local lint and tests rerun
nickp60
committed
fe0ac38

Commits on Jul 30, 2026

Code review for #52 (#68)
vinisalazar
authored
489dd49
Template update for nf-core/tools version 4.1.0
nickp60
committed
f70c3ed
merged 4.1.0 template
nickp60
committed
9acfcca

Commits on Jul 31, 2026

Fix DIAMOND db intake (#71)
vinisalazar
authored
f8607a3
Feat/cite (#72)

nickp60
and
sapunyangkut
authored
4d53c0c

Commits on Aug 3, 2026

Fix eggNOG-mapper database integration (#74)
vinisalazar
authored
a0d5bcc

Commits on Aug 4, 2026

WIP address outstanding comments
nickp60
committed
0693820
WIP addressing more comments; update profile snapshot
nickp60
committed
04a93a7
lint, address more comments
nickp60
committed
e6e396a
prek
nickp60
committed
c03cfbf

Commits on Aug 5, 2026

Address review follow-ups from PR #52

vinisalazar
and
jonasscheid
committed
77674e4
Merge pull request #77 from vinisalazar/fix/pr52-review-followups
vinisalazar
authored
8726325

Commits on Aug 11, 2026

Raise singularity pull timeout to 60m in test profiles
vinisalazar
committed
737fb89
Drop FastQC and defer read preprocessing to v1.1.0
vinisalazar
committed
c08987a

Commits on Aug 25, 2026

Move input validation to pipeline initialisation
vinisalazar
committed
228645a
Tidy local humann4 modules and subworkflow headers
vinisalazar
committed
e7c8691
Move test process config into conf/test.config
vinisalazar
committed
d3a8ec1
Rework usage and output documentation
vinisalazar
committed
1dc7f47
Simplify metro map
vinisalazar
committed
0873fd4

Commits on Sep 1, 2026

Redraw metro map with one line per input type
vinisalazar
committed
07bed54

Commits on Sep 2, 2026

Merge branch 'dev' into nf-core-template-merge-4.1.0
nickp60
authored
ec5fb1f
update modules and subworkflows
nickp60
committed
0804cb9
update snapshot for updated rgi/bwt
nickp60
committed
5b4a051

Commits on Sep 3, 2026

Merge pull request #80 from nf-core/nf-core-template-merge-4.1.0
nickp60
authored
472757a

Commits on Sep 4, 2026

Correct why mi-faser is off in the megatest
vinisalazar
committed
8de2886
Move the run endedness check to pipeline initialisation
vinisalazar
committed
59059c4
Draw the metro map junctions in the trunk colour
vinisalazar
committed
46e7c54
Say what beta means for DIAMOND and eggNOG-mapper
vinisalazar
committed
de63536
Drop a paragraph duplicated by the template merge
vinisalazar
committed
19c6534
Activate mifaser in test_full config
vinisalazar
committed
a8101ed

Commits on Sep 14, 2026

wip testing megatests with new samplesheet
nickp60
committed
b1e2b0d
fix bad run args
nickp60
committed
58d8d59

Commits on Sep 15, 2026

disable mpa in full tests
nickp60
committed
9525f43

Commits on Sep 17, 2026

remove temp paths for full tests
nickp60
committed
5b44f88