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feat: Add Claude Code hooks for automated testing and linting #3774

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ac89aba
feat: nf-core modules bump-version supports specifying the toolkit
nh13 Jun 5, 2025
a5b9730
chore: add unit test
nh13 Jun 7, 2025
c595d2e
update tests
nh13 Jun 8, 2025
279daf2
fix
nh13 Jun 8, 2025
5f27df3
fix
nh13 Jun 8, 2025
05c52e6
Support modules with exec: blocks
muffato Jun 20, 2025
6975c28
[automated] Update CHANGELOG.md
nf-core-bot Jun 20, 2025
2cff862
fix variable names and make dry_run a valid paramter
mashehu Jul 1, 2025
c08e81f
switch logic: no need for trailing backslash
mashehu Jul 1, 2025
e155906
Merge branch 'dev' of github.com:nf-core/tools into feat/bump-version…
mashehu Jul 1, 2025
6dccb6d
fix argument syntax
mashehu Jul 1, 2025
1896876
fix ruff linting
mashehu Jul 1, 2025
cdda107
test(#3590): Copy tests over from env sorter
edmundmiller May 29, 2025
54925f9
test(#3590): Refactor tests for environment.yml sorting and error han…
edmundmiller May 29, 2025
806f935
fint(#3590): Enhance environment.yml handling and sorting
edmundmiller May 30, 2025
945c115
refactor(#3590): Replace ruamel.yaml with PyYAML for environment.yml …
edmundmiller May 30, 2025
c62ccb9
test(#3590): Move integration tests to new lint test file
edmundmiller May 30, 2025
feabc68
test(#3590): Update dependency order on a test
edmundmiller May 30, 2025
e4026f3
Revert "refactor(#3590): Replace ruamel.yaml with PyYAML for environm…
edmundmiller May 30, 2025
d8eff3c
fix(#3590): Having first pip and then immediately followed by pip dep…
edmundmiller May 30, 2025
1d06957
refactor(#3590): Simplify environment.yml handling by removing channe…
edmundmiller May 30, 2025
8c4839c
style: Clean up parameterized tests
edmundmiller May 30, 2025
b6803c3
test(#3590): Refactor environment.yml tests with factory fixtures
edmundmiller May 30, 2025
c758daf
style: Fix code linting
edmundmiller May 30, 2025
c901b4c
chore: Add integration marker to pytest configuration
edmundmiller Jun 3, 2025
4b8226d
fix(test): Update assertion in environment.yml sorting test to use li…
edmundmiller Jun 3, 2025
ede037b
fix(modules): Check if they are not the exact same lines
edmundmiller Jul 1, 2025
2f3d236
Add module install autocompletion
Jul 7, 2025
e906671
Add completion for all modules subcommand
Jul 7, 2025
ebafbfe
Add completion and test
LouisLeNezet Jul 8, 2025
c14dfab
Merge branch 'dev' into autocomplete
LouisLeNezet Jul 8, 2025
115ac77
Update Changelog
LouisLeNezet Jul 8, 2025
485c4e7
Fix code
LouisLeNezet Jul 8, 2025
cba8dce
Fix order import
LouisLeNezet Jul 8, 2025
de2f800
Fix linting
LouisLeNezet Jul 8, 2025
253aed1
Update test
LouisLeNezet Jul 8, 2025
67b1504
Merge branch 'dev' into autocomplete
LouisLeNezet Jul 8, 2025
81e58c5
Update changelog
LouisLeNezet Jul 8, 2025
b501f41
Check for error
LouisLeNezet Jul 8, 2025
318b216
Add test with ctx object
LouisLeNezet Jul 8, 2025
4f9d937
bump to 3.4.0dev
mashehu Jul 8, 2025
81484bb
Move all script to component_completion
Jul 8, 2025
bc50d83
Add pipeline real completion test
Jul 8, 2025
28b76a4
Merge pull request #3670 from mashehu/bump-to-3_4_0dev
mirpedrol Jul 9, 2025
d1a6d4f
Change location pipeline autocompletion and use gitlab dummy
Jul 9, 2025
fb6414e
Fix import
Jul 9, 2025
9ac6dd8
Update pipelines completion test
Jul 9, 2025
8517758
Update test
Jul 9, 2025
9c887aa
Update test
Jul 9, 2025
3b4e499
Fix test
Jul 9, 2025
1e2a06d
Merge branch 'dev' into autocomplete
LouisLeNezet Jul 9, 2025
ef427b5
don't read param expressions with spaces as params
mirpedrol Jul 10, 2025
bb13b04
[automated] Update CHANGELOG.md
nf-core-bot Jul 10, 2025
587b816
add test for fetch_wf_config utils
mirpedrol Jul 10, 2025
3e51a72
Merge pull request #3674 from mirpedrol/schema-params-regex
mirpedrol Jul 15, 2025
92e1325
Remove unecessary mocked test
LouisLeNezet Jul 15, 2025
ad1b451
Merge branch 'dev' into autocomplete
LouisLeNezet Jul 15, 2025
98193bc
Merge pull request #3660 from LouisLeNezet/autocomplete
LouisLeNezet Jul 15, 2025
840d0d9
Merge branch 'dev' into module_exec
muffato Jul 16, 2025
5081480
Update marocchino/sticky-pull-request-comment digest to 7737449 (#3681)
renovate[bot] Jul 21, 2025
e6cc401
With cross-org repos, components can be dictionaries whose (only) key…
muffato Jul 15, 2025
ae7ca23
[automated] Update CHANGELOG.md
nf-core-bot Jul 15, 2025
7f2b96b
Migrate config .github/renovate.json5
renovate[bot] Jul 21, 2025
27d8ebe
Merge branch 'dev' of github.com:nf-core/tools into env-sorting
mashehu Jul 21, 2025
186ca11
make the tests more similar to the rest of the testing structure
mashehu Jul 21, 2025
7433611
Merge pull request #3591 from nf-core/env-sorting
edmundmiller Jul 21, 2025
30ad303
Update .nftignore
jonasscheid Jul 22, 2025
8a64840
update multiQC to 1.30
jonasscheid Jul 23, 2025
a6c148f
update pipelien template default snapshot with new mqc llm.txt output
jonasscheid Jul 24, 2025
ec47974
update snapshots
jonasscheid Jul 24, 2025
ab6cd6a
Merge pull request #3686 from jonasscheid/nftestignore-mqc-llmstxt
jonasscheid Jul 24, 2025
95ec76d
refactor: Split up test_lint tests to match modules lint structure
edmundmiller May 30, 2025
8d90306
test: Add new lint tests for module changes, deprecations, todos, and…
edmundmiller May 30, 2025
8deb75a
build: Set ruff as default editor
edmundmiller May 30, 2025
92e62b6
style: Run ruff format
edmundmiller May 30, 2025
2dfcb1e
Merge pull request #3682 from nf-core/renovate/migrate-config
edmundmiller Jul 24, 2025
c041f82
test: Enhance test for linting by checking for test_snap_md5sum in pa…
edmundmiller May 30, 2025
869a8a3
clean up test_main_nf.py
mashehu Jul 28, 2025
5c6b7d6
Merge branch 'dev' of github.com:nf-core/tools into feat/bump-version…
mashehu Jul 28, 2025
9a4f113
[automated] Update CHANGELOG.md
nf-core-bot Jul 28, 2025
28192a0
fix tests
mashehu Jul 28, 2025
7af69f1
Merge pull request #3608 from nf-core/feat/bump-versions-for-sub-modules
mashehu Jul 28, 2025
378f522
feat\!: replace arm profile with arm64 and emulate_amd64 profiles
edmundmiller Jul 28, 2025
6d10567
[automated] Update CHANGELOG.md
nf-core-bot Jul 28, 2025
1422ae1
add a description of allowed enum values to the docs
shenkers Jul 29, 2025
8749094
add changelog update
shenkers Jul 29, 2025
ff2ba34
Update nf_core/pipelines/schema.py
shenkers Jul 30, 2025
beb29d1
Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.7
renovate[bot] Aug 1, 2025
2e16fa5
Update pre-commit hook pre-commit/mirrors-mypy to v1.17.1
renovate[bot] Aug 1, 2025
b204343
Update dependency textual to v5
renovate[bot] Aug 1, 2025
c1044fc
[automated] Update CHANGELOG.md
nf-core-bot Aug 1, 2025
b3c6411
[automated] Update CHANGELOG.md
nf-core-bot Aug 1, 2025
8d0ad78
[automated] Update CHANGELOG.md
nf-core-bot Aug 1, 2025
9bff2b9
Merge pull request #3680 from nf-core/crossorg_yaml_validation
mirpedrol Aug 1, 2025
2872af9
Merge branch 'dev' into module_exec
mirpedrol Aug 1, 2025
1e3a7da
Merge pull request #3633 from nf-core/module_exec
mirpedrol Aug 1, 2025
715508c
Update python:3.13-slim Docker digest to 4c2cf99 (#3700)
renovate[bot] Aug 12, 2025
59b0e17
update textual snapshots
mirpedrol Aug 12, 2025
784da0e
update textual snapshots
mirpedrol Aug 12, 2025
b3e2522
Merge branch 'dev' into renovate/textual-5.x
mirpedrol Aug 12, 2025
03b166f
Merge pull request #3693 from shenkers/addAllowedEnumValuesToDocs
mirpedrol Aug 12, 2025
4cab74a
Update GitHub Actions to v5 (#3702)
renovate[bot] Aug 12, 2025
224b7df
Merge branch 'dev' into renovate/pre-commit-mirrors-mypy-1.x
mirpedrol Aug 12, 2025
d1e427a
Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x
mirpedrol Aug 12, 2025
45a3f4c
Merge pull request #3698 from nf-core/renovate/pre-commit-mirrors-myp…
mirpedrol Aug 12, 2025
808aaeb
Merge branch 'dev' into renovate/astral-sh-ruff-pre-commit-0.x
mirpedrol Aug 12, 2025
3848c13
Merge pull request #3697 from nf-core/renovate/astral-sh-ruff-pre-com…
mirpedrol Aug 12, 2025
9193958
Merge branch 'dev' into renovate/textual-5.x
mirpedrol Aug 12, 2025
c3b528d
Merge pull request #3699 from nf-core/renovate/textual-5.x
mirpedrol Aug 13, 2025
92cce0b
test: Implement module lint tests and consolidate MockModuleLint class
edmundmiller Aug 12, 2025
4d812e4
fix: Handle corrupted JSON cache files gracefully in utils
edmundmiller Aug 13, 2025
83b6237
refactor: Consolidate module installation in test setUp methods
edmundmiller Aug 14, 2025
b2bd61b
Merge branch 'dev' into rename-arm
edmundmiller Aug 19, 2025
b926332
Merge pull request #3689 from nf-core/rename-arm
edmundmiller Aug 19, 2025
21c78e6
remove workflow.trace from nf-test snapshot to avoid errors due to in…
mirpedrol Aug 22, 2025
2e2cb7a
remove requirements duplication
mirpedrol Aug 22, 2025
2c01ade
[automated] Update CHANGELOG.md
nf-core-bot Aug 22, 2025
80cfe38
ignore files in gitignore also for pipeline_if_empty_null lint test
mirpedrol Aug 22, 2025
4792cf2
[automated] Update CHANGELOG.md
nf-core-bot Aug 22, 2025
8086e72
update all pipeline snapshots
mirpedrol Aug 22, 2025
093a173
add GHA to update template nf-test snapshots
mirpedrol Aug 25, 2025
40313ba
[automated] Update CHANGELOG.md
nf-core-bot Aug 25, 2025
b0583d0
Merge pull request #3721 from mirpedrol/workflow-trace
mirpedrol Aug 25, 2025
aeb1cc9
Merge branch 'dev' into ignore-gitignore-files
mirpedrol Aug 25, 2025
3201d00
Merge branch 'dev' into update-template-snapshots
mirpedrol Aug 25, 2025
f768e9d
handle error when .gitignore does not exist
mirpedrol Aug 25, 2025
ef628f3
update gha triggers for snapshot updates
mirpedrol Aug 25, 2025
283e8c5
Merge pull request #3722 from mirpedrol/ignore-gitignore-files
mirpedrol Aug 25, 2025
9e03edc
update changelog
mirpedrol Aug 25, 2025
22a879d
Merge pull request #3723 from mirpedrol/update-template-snapshots
mirpedrol Aug 26, 2025
584527b
test: Improve test structure and remove setUp assertions
edmundmiller Aug 26, 2025
2bc29fd
Merge pull request #3592 from nf-core/refactor-module-lint-test
edmundmiller Aug 26, 2025
a35f9bc
feat: Add lint check for version snapshot content validation
edmundmiller Jul 11, 2025
ff546d6
refactor: Improve version snapshot content validation with enhanced r…
edmundmiller Aug 26, 2025
11bcdcb
fix: Fix version content validation loop logic and improve test coverage
edmundmiller Aug 26, 2025
1ddf9ce
fix: Address PR review feedback
edmundmiller Sep 27, 2025
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2 changes: 1 addition & 1 deletion .github/renovate.json5
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$schema: "https://docs.renovatebot.com/renovate-schema.json",
extends: ["github>nf-core/ops//.github/renovate/default.json5"],
ignorePaths: ["**/nf_core/pipeline-template/modules/nf-core/**"],
baseBranches: ["dev"],
baseBranchPatterns: ["dev"],
packageRules: [
{
matchDatasources: ["docker"],
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2 changes: 1 addition & 1 deletion .github/snapshots/adaptivecard.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/changelog.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/ci.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/citations.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/code_linters.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/codespaces.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/default.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/documentation.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/email.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
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"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/fastqc.nf.test.snap
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{
"-profile test": {
"content": [
1,
{
"Workflow": {
"my-prefix/testpipeline": "v1.0.0dev"
Expand All @@ -11,6 +10,7 @@
"multiqc",
"multiqc/multiqc_data",
"multiqc/multiqc_data/BETA-multiqc.parquet",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/github_badges.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/gitpod.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/gpu.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/igenomes.nf.test.snap
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{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/license.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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1 change: 0 additions & 1 deletion .github/snapshots/modules.nf.test.snap
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{
"-profile test": {
"content": [
0,
null,
[
"pipeline_info"
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1 change: 0 additions & 1 deletion .github/snapshots/multiqc.nf.test.snap
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{
"-profile test": {
"content": [
3,
null,
[
"fastqc",
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2 changes: 1 addition & 1 deletion .github/snapshots/nf_core_configs.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/nf_schema.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/rocrate.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/seqera_platform.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/slackreport.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/snapshots/vscode.nf.test.snap
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@@ -1,7 +1,6 @@
{
"-profile test": {
"content": [
4,
{
"FASTQC": {
"fastqc": "0.12.1"
Expand Down Expand Up @@ -38,6 +37,7 @@
"multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
"multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
"multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
"multiqc/multiqc_data/llms-full.txt",
"multiqc/multiqc_data/multiqc.log",
"multiqc/multiqc_data/multiqc_citations.txt",
"multiqc/multiqc_data/multiqc_data.json",
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2 changes: 1 addition & 1 deletion .github/workflows/changelog.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
)

steps:
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
with:
token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}

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2 changes: 1 addition & 1 deletion .github/workflows/create-lint-wf.yml
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Expand Up @@ -42,7 +42,7 @@ jobs:
export NXF_WORK=$(pwd)

# Get the repo code
- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
name: Check out source-code repository

# Set up nf-core/tools
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4 changes: 2 additions & 2 deletions .github/workflows/create-test-lint-wf-template.yml
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Expand Up @@ -32,7 +32,7 @@ jobs:
all_features: ${{ steps.create_matrix.outputs.matrix }}
steps:
- name: checkout
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
- name: Create Matrix
id: create_matrix
run: |
Expand All @@ -56,7 +56,7 @@ jobs:

steps:
- name: Check out source-code repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5

- name: Set up Python 3.13
uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
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