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resolve conflicts with our config
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‎.editorconfig

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Original file line numberDiff line numberDiff line change
@@ -8,5 +8,5 @@ trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{md,yml,yaml}]
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[*.{md,yml,yaml,cff}]
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indent_size = 2

‎.github/CODEOWNERS

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@@ -0,0 +1,6 @@
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**/ceci_** @MartinGrignard
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**/giga** @MartinGrignard
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**/shu_bmrc** @lquayle88
4+
**/utd_ganymede** @edmundmiller @alyssa-ab
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**/unsw_katana** @jscgh
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**/seadragon** @jiawku

‎.github/PULL_REQUEST_TEMPLATE.md

+2-1
Original file line numberDiff line numberDiff line change
@@ -16,9 +16,10 @@ Steps for adding a new config profile:
1616
- [ ] Add your custom profile to the `nfcore_custom.config` file in the top-level directory
1717
- [ ] Add your custom profile to the `README.md` file in the top-level directory
1818
- [ ] Add your profile name to the `profile:` scope in `.github/workflows/main.yml`
19+
- [ ] OPTIONAL: Add your custom profile path and GitHub user name to `.github/CODEOWNERS` (`**/<custom-profile>** @<github-username>`)
1920

2021
<!--
21-
If you require/still waiting for a review, please feel free to request from @nf-core/configs-team
22+
If you require/still waiting for a review, please feel free to request a review from @nf-core/maintainers
2223
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Please see uploading to`nf-core/configs` for more details:
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https://github.com/nf-core/configs#uploading-to-nf-coreconfigs

‎.github/generate_codeowners.sh

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@@ -0,0 +1,22 @@
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#!/usr/bin/env bash
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3+
CONFIGS=$(fd . -e .config 'conf/')
4+
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output_file=".github/CODEOWNERS"
6+
rm $output_file
7+
8+
for file in $CONFIGS; do
9+
# Get the line of the file that starts with config_profile_contact
10+
line=$(rg "config_profile_contact" "$file")
11+
# and then get the username after the @ and remove anything after it
12+
username=$(echo "$line" | sed 's/^.*@/@/g')
13+
# Remove the )'
14+
username=$(echo "$username" | sed 's/).*$//g')
15+
16+
# Get the insitute name
17+
# conf/<institute>.config
18+
institute=$(echo "$file" | sed 's/^.*\///g' | sed 's/\.config$//g')
19+
20+
# # Remove quotes from authors
21+
echo "**$institute**" $username >> $output_file
22+
done

‎.github/workflows/fix-linting.yml

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@@ -0,0 +1,89 @@
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name: Fix linting from a comment
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on:
3+
issue_comment:
4+
types: [created]
5+
6+
jobs:
7+
fix-linting:
8+
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
9+
if: >
10+
contains(github.event.comment.html_url, '/pull/') &&
11+
contains(github.event.comment.body, '@nf-core-bot fix linting') &&
12+
github.repository == 'nf-core/configs'
13+
runs-on: ubuntu-latest
14+
steps:
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# Use the @nf-core-bot token to check out so we can push later
16+
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
19+
20+
# indication that the linting is being fixed
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- name: React on comment
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
24+
comment-id: ${{ github.event.comment.id }}
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reactions: eyes
26+
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# Action runs on the issue comment, so we don't get the PR by default
28+
# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
32+
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
33+
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# Install and run pre-commit
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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with:
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python-version: 3.11
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- name: Install pre-commit
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run: pip install pre-commit
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- name: Run pre-commit
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id: pre-commit
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run: pre-commit run --all-files
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continue-on-error: true
46+
47+
# indication that the linting has finished
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- name: react if linting finished succesfully
49+
if: steps.pre-commit.outcome == 'success'
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uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
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comment-id: ${{ github.event.comment.id }}
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reactions: "+1"
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- name: Commit & push changes
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id: commit-and-push
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if: steps.pre-commit.outcome == 'failure'
58+
run: |
59+
git config user.email "core@nf-co.re"
60+
git config user.name "nf-core-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Fix code linting"
65+
git push
66+
67+
- name: react if linting errors were fixed
68+
id: react-if-fixed
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if: steps.commit-and-push.outcome == 'success'
70+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
72+
comment-id: ${{ github.event.comment.id }}
73+
reactions: hooray
74+
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- name: react if linting errors were not fixed
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if: steps.commit-and-push.outcome == 'failure'
77+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
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comment-id: ${{ github.event.comment.id }}
80+
reactions: confused
81+
82+
- name: react if linting errors were not fixed
83+
if: steps.commit-and-push.outcome == 'failure'
84+
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
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with:
86+
issue-number: ${{ github.event.issue.number }}
87+
body: |
88+
@${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
89+
See [CI log](https://github.com/nf-core/configs/actions/runs/${{ github.run_id }}) for more details.

‎.github/workflows/linting.yml

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@@ -1,22 +1,21 @@
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name: Code Linting
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name: Lint tools code formatting
22
on:
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pull_request:
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push:
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branches:
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- master
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pull_request:
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# Cancel if a newer run is started
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
11+
cancel-in-progress: true
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813
jobs:
9-
prettier:
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pre-commit:
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runs-on: ubuntu-latest
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
1118
steps:
12-
- name: Check out repository
13-
uses: actions/checkout@v2
14-
15-
- name: Install NodeJS
16-
uses: actions/setup-node@v2
17-
18-
- name: Install Prettier
19-
run: npm install -g prettier
20-
21-
- name: Run Prettier --check
22-
run: prettier --check ${GITHUB_WORKSPACE}
19+
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
20+
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: pre-commit/action@v3.0.1

‎.github/workflows/linting_comment.yml

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name: nf-core linting comment
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# This workflow is triggered after the linting action is complete
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# It posts an automated comment to the PR, even if the PR is coming from a fork {%- raw %}
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on:
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workflow_run:
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workflows: ["nf-core linting"]
8+
9+
jobs:
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test:
11+
runs-on: ubuntu-latest
12+
steps:
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- name: Download lint results
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uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
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with:
16+
workflow: linting.yml
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workflow_conclusion: completed
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19+
- name: Get PR number
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id: pr_number
21+
run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
22+
23+
- name: Post PR comment
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uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
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with:
26+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
27+
number: ${{ steps.pr_number.outputs.pr_number }}
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path: linting-logs/lint_results.md

‎.github/workflows/main.yml

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@@ -2,20 +2,25 @@ name: Configs tests
22

33
on: [pull_request, push]
44

5+
# Cancel if a newer run is started
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concurrency:
7+
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
8+
cancel-in-progress: true
9+
510
jobs:
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test_all_profiles:
712
runs-on: ubuntu-latest
813
name: Check if all profiles are tested
914
steps:
10-
- uses: actions/checkout@v1
15+
- uses: actions/checkout@v4
1116
- name: Check whether profiles are all tested
1217
run: python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
1318

1419
check_nextflow_config:
1520
runs-on: ubuntu-latest
1621
name: Check if nextflow config runs in repository root
1722
steps:
18-
- uses: actions/checkout@v1
23+
- uses: actions/checkout@v4
1924
- name: Install Nextflow
2025
run: |
2126
wget -qO- get.nextflow.io | bash
@@ -30,67 +35,154 @@ jobs:
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matrix:
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profile:
3237
- "abims"
38+
- "adcra"
3339
- "alice"
40+
- "apollo"
41+
- "arcc"
3442
- "aws_tower"
3543
- "awsbatch"
3644
- "azurebatch"
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- "bi"
3846
- "bigpurple"
47+
- "bih"
3948
- "binac"
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- "biohpc_gen"
50+
- "biowulf"
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- "bluebear"
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- "cambridge"
42-
- "leicester"
4353
- "cbe"
4454
- "ccga_dx"
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- "ccga_med"
56+
- "ceci_dragon2"
57+
- "ceci_nic5"
58+
- "cedars"
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- "ceres"
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- "cfc"
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- "cfc_dev"
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- "cheaha"
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- "computerome"
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- "create"
65+
- "crg"
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- "crick"
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- "crukmi"
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- "csiro_petrichor"
69+
- "daisybio"
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- "denbi_qbic"
71+
- "dkfz"
5272
- "ebc"
73+
- "ebi_codon"
74+
- "ebi_codon_slurm"
5375
- "eddie"
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- "embl_hd"
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- "engaging"
78+
- "einstein"
79+
- "ethz_euler"
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- "eva"
5581
- "fgcz"
82+
- "fub_curta"
5683
- "genotoul"
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- "genouest"
85+
- "giga"
5886
- "gis"
5987
- "google"
88+
- "googlebatch"
89+
- "googlels"
6090
- "hasta"
61-
- "hebbe"
91+
- "hki"
92+
- "hypatia"
6293
- "icr_davros"
6394
- "ifb_core"
95+
- "imb"
96+
- "ilifu"
6497
- "imperial"
98+
- "incliva"
99+
- "ipop_up"
100+
- "janelia"
65101
- "jax"
102+
- "jex"
103+
- "unsw_katana"
104+
- "ku_sund_danhead"
105+
- "kaust"
106+
- "ki_luria"
107+
- "leicester"
66108
- "lugh"
67-
- "marvin"
109+
- "m3c"
68110
- "maestro"
111+
- "mana"
112+
- "marjorie"
113+
- "marvin"
114+
- "mccleary"
115+
- "medair"
116+
- "mjolnir_globe"
69117
- "mpcdf"
118+
- "mpcdf_viper"
70119
- "munin"
120+
- "nci_gadi"
71121
- "nu_genomics"
72-
- "nihbiowulf"
122+
- "nygc"
123+
- "nyu_hpc"
73124
- "oist"
74125
- "pasteur"
126+
- "pawsey_nimbus"
127+
- "pawsey_setonix"
128+
- "pdc_kth"
129+
- "pe2"
75130
- "phoenix"
76-
- "prince"
131+
- "psmn"
132+
- "qmul_apocrita"
77133
- "rosalind"
134+
- "rosalind_uge"
135+
- "roslin"
136+
- "sage"
78137
- "sahmri"
79138
- "sanger"
139+
- "scw"
140+
- "seadragon"
141+
- "seawulf"
80142
- "seg_globe"
143+
- "self_hosted_runner"
144+
- "shu_bmrc"
145+
- "software_license"
146+
- "stjude"
147+
- "tes"
148+
- "tigem"
149+
- "tubingen_apg"
150+
- "tufts"
151+
- "tuos_stanage"
152+
- "ucl_cscluster"
153+
- "ucl_myriad"
81154
- "uct_hpc"
155+
- "ucd_sonic"
156+
- "uge"
82157
- "unibe_ibu"
158+
- "unity"
159+
- "unc_lccc"
160+
- "unc_longleaf"
161+
- "uod_hpc"
83162
- "uppmax"
84163
- "utd_ganymede"
85-
- "utd_sysbio"
164+
- "uw_hyak_pedslabs"
86165
- "uzh"
166+
- "uzl_omics"
87167
- "vai"
168+
- "vsc_calcua"
169+
- "vsc_kul_uhasselt"
170+
- "vsc_ugent"
171+
- "wehi"
172+
- "wustl_htcf"
173+
- "xanadu"
174+
- "york_viking"
175+
88176
steps:
89-
- uses: actions/checkout@v1
90-
- name: Install Nextflow
91-
run: |
92-
wget -qO- get.nextflow.io | bash
93-
sudo mv nextflow /usr/local/bin/
177+
- uses: actions/checkout@v4
178+
- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
179+
with:
180+
distribution: "temurin"
181+
java-version: "17"
182+
- name: Set up Nextflow
183+
uses: nf-core/setup-nextflow@v2
184+
with:
185+
version: "latest-everything"
94186
- name: Check ${{ matrix.profile }} profile
95187
env:
96188
SCRATCH: "~"

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