Release v1.1.0 - #33

Merged

ToonRosseel merged 63 commits into

Aug 25, 2026

Commits on Mar 19, 2026

replace 'merge_reads' with 'cat_fastq'
matthdsm
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f5a6d5e
improve 'hotcount'
matthdsm
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7c3898d
linting
matthdsm
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4fec6f1
update modules
matthdsm
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ee45636
drop iGenomes
matthdsm
committed
540e98d
fix glaring issues with spothot
matthdsm
committed
1aa0280
busywork
matthdsm
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10a6447

Commits on Mar 23, 2026

fix fai_file for samtools_sort
ToonRosseel
committed
4787a40
fix fasta_fai for samtools_sort
ToonRosseel
committed
dd02b54
fix fai_file for samtools_sort
ToonRosseel
committed
48473c7
optimize hotcount process for expected output
ToonRosseel
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fa28e54
Merge branch 'fix/ditch_stuff' of https://github.com/nf-cmgg/report into fix/ditch_stuff
ToonRosseel
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a480dab
lowering memory needs
ToonRosseel
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16a30a7
fix CAT_FASTQ input bug
ToonRosseel
committed
afde803

Commits on Mar 24, 2026

lowering memory needs hotcount
ToonRosseel
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5f23c53
remove deprecated script
ToonRosseel
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3ad3fd0

Commits on Jun 24, 2026

cleanup docs
ToonRosseel
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b2ee9d9
Merge branch 'fix/ditch_stuff' of https://github.com/nf-cmgg/report into fix/ditch_stuff
ToonRosseel
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392b2f9
Merge branch 'dev' into fix/ditch_stuff
nvnieuwk
authored
c6ca843
Update docs/parameters.md

ToonRosseel
and
nvnieuwk
authored
ba937df
Update docs/usage.md

ToonRosseel
and
nvnieuwk
authored
8b99841

Commits on Jun 25, 2026

revert to old layout
ToonRosseel
committed
8e6151a
small doc updates
ToonRosseel
committed
1d9e38e

Commits on Jul 9, 2026

add pixi env + run prek
nvnieuwk
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056e652
fix default snap
nvnieuwk
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c93bd6e
fix varcov test input
nvnieuwk
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2080989
fix lint issues part 1
nvnieuwk
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d07cb63
fix lint issues part 2
nvnieuwk
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6614ea5
fix lint issues part 3
nvnieuwk
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f036e9a
prek
nvnieuwk
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2f53ad1
bump ci nf-test version
nvnieuwk
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4d5e881

Commits on Jul 10, 2026

Merge pull request #28 from nf-cmgg/fix/ditch_stuff
ToonRosseel
authored
aaebbb2

Commits on Jul 17, 2026

update changelog
ToonRosseel
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3653eca
bump version 1.1.0
ToonRosseel
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2ff1590
bump new multiqc version
ToonRosseel
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cf8633b
linting
ToonRosseel
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4f2edf2
Merge pull request #30 from nf-cmgg/add_release_notes
nvnieuwk
authored
92a34b2
fix nf-core yaml
nvnieuwk
committed
5acabd2
Template update for nf-core/tools version 4.0.2
nvnieuwk
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637595d
Merge branch 'TEMPLATE' into bump/nf-core
nvnieuwk
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0e726df
make workflow run again
nvnieuwk
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8b24c81
fix nf-core lint
nvnieuwk
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db01b16
prek
nvnieuwk
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0fd63f0
bump changelog
nvnieuwk
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9ac74d1
fix nf-test version
nvnieuwk
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ad8219e
ignore nf-cmgg configs in test
nvnieuwk
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1a72a48
Merge pull request #31 from nf-cmgg/bump/nf-core
nvnieuwk
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328c5ee
add targeted.fai parameter + disable pacvar_repeat
nvnieuwk
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e0c120c
improvements to targeted
nvnieuwk
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354f218
simplify flow a bit
nvnieuwk
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285d06f
fix snapshot
nvnieuwk
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4fe618f
validate queries earlier
nvnieuwk
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5bd5215
Merge pull request #32 from nf-cmgg/fix/targeted
nvnieuwk
authored
699a3cc

Commits on Jul 23, 2026

Revise changelog for v1.1.0 release
ToonRosseel
authored
ed39de3
Update date format in CHANGELOG for v1.1.0
ToonRosseel
authored
75af467
update docs targeted tool
ToonRosseel
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32f749a
fix lint issue
ToonRosseel
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357e2bc
add rnafusion docs
nvnieuwk
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a8a4da2

Commits on Jul 30, 2026

Merge pull request #34 from nf-cmgg/docs
nvnieuwk
authored
bc80036

Commits on Aug 6, 2026

revert nf-cmgg configs to nf-core configs
nvnieuwk
committed
ff5b4fd

Commits on Aug 17, 2026

Merge pull request #35 from nf-cmgg/revert/nf-cmgg-configs
nvnieuwk
authored
5dd3d3a

Commits on Aug 25, 2026

Remove Conda setup from nf-test action
nvnieuwk
authored
45a4480
Update workflow to exclude 'conda' profile
nvnieuwk
authored
d16558e