Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add GHA to periodically update class subworkflows and open a PR #5

Open
wants to merge 8 commits into
base: poc-classes
Choose a base branch
from
Open

add GHA to periodically update class subworkflows and open a PR #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
981429c
add GHA to periodically update class subworkflows and open a PR
mirpedrol Nov 27, 2024
c498a7e
update modules and subworkflows
mirpedrol Dec 5, 2024
04861e9
update editorconfig version
mirpedrol Dec 5, 2024
82799ff
Merge branch 'poc-classes' into automated-benchmarking
mirpedrol Dec 5, 2024
4b66d36
check if files actually changed
mirpedrol Jan 8, 2025
7955bba
remove old functions included
mirpedrol Jan 8, 2025
9c346b8
add alignment param to all tests
mirpedrol Jan 8, 2025
b0b904a
add resourceLimits to all tests
mirpedrol Jan 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions .editorconfig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,3 +31,6 @@ indent_size = unset
# ignore python and markdown
[*.{py,md}]
indent_style = unset

[*.nf.test]
insert_final_newline = false
48 changes: 48 additions & 0 deletions .github/workflows/update-class-subworkflows.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
name: Update class subworkflows

on:
schedule:
- cron: "0 0 * * *" # Run every day at midnight
workflow_dispatch:

jobs:
update_modules:
runs-on: ubuntu-latest

steps:
- name: Checkout repository
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

- name: Set up Python
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
with:
python-version: "3.x"

- name: Install nf-core
run: pip install nf-core

- name: Update subworkflows
run: nf-core subworkflows --git-remote https://github.com/mirpedrol/class-modules.git update --all --no-preview --update-deps

- name: Check if there are changes
run: |
git diff --exit-code ${GITHUB_WORKSPACE} || echo "changed=YES" >> $GITHUB_ENV
echo "Files changed: ${{ env.changed }}"

# Commit the changes
- name: Commit changes
if: env.changed == 'YES'
run: |
git config user.email "[email protected]"
git config user.name "mirpedrol"
git add .
git status
git commit -m "[automated] Update class subworkflows"

# Open a new PR to dev with the changes
- name: Create PR
if: env.changed == 'YES'
run: |
git checkout -b automated-update-class-subworkflows
git push origin automated-update-class-subworkflows
gh pr create --title "Update class subworkflows" --body "This PR updates the class subworkflows form the mirpedrol/class-modules repo" --base poc-classes --head automated-update-class-subworkflows
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ repos:
- [email protected]

- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: "2.7.3"
rev: "3.0.3"
hooks:
- id: editorconfig-checker
alias: ec
9 changes: 8 additions & 1 deletion conf/test_full.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,13 @@

----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 2,
memory: '6.GB',
time: '6.h'
]
}
params {
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'
Expand All @@ -27,4 +33,5 @@ params {

// Input data for full size test
input = params.pipelines_testdata_base_path + 'multiplesequencealign/samplesheet/v1.0/samplesheet_full.csv'
alignment = 'clustalo/align'
}
14 changes: 8 additions & 6 deletions conf/test_parameters.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,20 +9,22 @@

----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 2,
memory: '6.GB',
time: '6.h'
]
}
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

skip_stats = true
skip_eval = true
skip_compression = false

// Input data
input = params.pipelines_testdata_base_path + 'multiplesequencealign/samplesheet/v1.0/samplesheet_test_af2.csv'
alignment = 'clustalo/align'
}
14 changes: 8 additions & 6 deletions conf/test_pdb.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,17 @@

----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 2,
memory: '6.GB',
time: '6.h'
]
}
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

skip_stats = true
calc_irmsd = true
calc_sp = false
Expand All @@ -28,4 +29,5 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'multiplesequencealign/samplesheet/v1.0/samplesheet_test.csv'
alignment = 'clustalo/align'
}
36 changes: 18 additions & 18 deletions modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,42 +7,42 @@
"mirpedrol": {
"clustalo/align": {
"branch": "main",
"git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_alignment"]
},
"clustalo/guidetree": {
"branch": "main",
"git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["modules", "msa_guidetree"]
},
"clustalo/treealign": {
"branch": "main",
"git_sha": "3987b7c6d9bcfc037c4976142b126c18558b0aed",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_treealign"]
},
"famsa/align": {
"branch": "main",
"git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_alignment"]
},
"famsa/guidetree": {
"branch": "main",
"git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_guidetree"]
},
"famsa/treealign": {
"branch": "main",
"git_sha": "3987b7c6d9bcfc037c4976142b126c18558b0aed",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_treealign"]
},
"kalign/align": {
"branch": "main",
"git_sha": "34e891b859086dd03e52e79abcf47b3863fcb3cb",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_alignment"]
},
"learnmsa/align": {
"branch": "main",
"git_sha": "caf37f3ee943a8101000b25ba502f038f8bfeb87",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_alignment"]
},
"mafft": {
Expand All @@ -52,17 +52,17 @@
},
"magus/align": {
"branch": "main",
"git_sha": "caf37f3ee943a8101000b25ba502f038f8bfeb87",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_alignment"]
},
"magus/guidetree": {
"branch": "main",
"git_sha": "519be3b194f5e2e271436398c1646c538867fe3e",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_guidetree"]
},
"magus/treealign": {
"branch": "main",
"git_sha": "3987b7c6d9bcfc037c4976142b126c18558b0aed",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_treealign"]
},
"muscle5/super5": {
Expand All @@ -72,12 +72,12 @@
},
"tcoffee/align": {
"branch": "main",
"git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_alignment"]
},
"tcoffee/treealign": {
"branch": "main",
"git_sha": "3987b7c6d9bcfc037c4976142b126c18558b0aed",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["msa_treealign"]
}
}
Expand All @@ -86,17 +86,17 @@
"mirpedrol": {
"msa_alignment": {
"branch": "main",
"git_sha": "927094f07130b8fa3ac0b8d1f46fd7d252809418",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["subworkflows"]
},
"msa_guidetree": {
"branch": "main",
"git_sha": "4748294a96583ecb2c3952e7f81aca426386cc0b",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["subworkflows"]
},
"msa_treealign": {
"branch": "main",
"git_sha": "0165b5b51bb1fe396a90c2db93c1f4e70b170816",
"git_sha": "c9e7bf0f32e3867e1b208b03ca69acb086ff97ca",
"installed_by": ["subworkflows"]
}
}
Expand Down Expand Up @@ -157,12 +157,12 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
"git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
"git_sha": "d588e574e40a8aeba3636e2b766358091bfa3aa0",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
Expand Down
4 changes: 2 additions & 2 deletions modules/mirpedrol/clustalo/align/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
"""
}
}
Expand Down
2 changes: 1 addition & 1 deletion modules/mirpedrol/clustalo/guidetree/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/yaml-schema.json
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/meta-schema.json
name: "clustalo_guidetree"
description: Renders a guidetree in clustalo
keywords:
Expand Down
7 changes: 3 additions & 4 deletions modules/mirpedrol/clustalo/guidetree/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
"""
}
}
Expand All @@ -29,5 +29,4 @@ nextflow_process {
)
}
}

}
}
8 changes: 4 additions & 4 deletions modules/mirpedrol/clustalo/treealign/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
"""
}
}
Expand All @@ -30,8 +30,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
input[1] = CLUSTALO_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_summary'], tree]}
"""
}
Expand Down
2 changes: 1 addition & 1 deletion modules/mirpedrol/famsa/align/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/yaml-schema.json
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/meta-schema.json
name: "famsa_align"
description: Aligns sequences using FAMSA
keywords:
Expand Down
4 changes: 2 additions & 2 deletions modules/mirpedrol/famsa/align/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
"""
}
}
Expand Down
2 changes: 1 addition & 1 deletion modules/mirpedrol/famsa/guidetree/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/yaml-schema.json
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/meta-schema.json
name: "famsa_guidetree"
description: Renders a guidetree in famsa
keywords:
Expand Down
6 changes: 3 additions & 3 deletions modules/mirpedrol/famsa/guidetree/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
"""
}
}
Expand All @@ -29,4 +29,4 @@ nextflow_process {
)
}
}
}
}
2 changes: 1 addition & 1 deletion modules/mirpedrol/famsa/treealign/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/yaml-schema.json
# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/modules/meta-schema.json
name: "famsa_treealign"
description: Aligns sequences using FAMSA
keywords:
Expand Down
8 changes: 4 additions & 4 deletions modules/mirpedrol/famsa/treealign/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
"""
}
}
Expand All @@ -30,8 +30,8 @@ nextflow_process {
process {
"""
input[0] = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
]
input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_summary'], tree]}
"""
}
Expand Down
Loading
Loading