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Test PR #49

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bd52ca8
Add line
code-flowbio Sep 3, 2024
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code-flowbio Sep 3, 2024
d3b1a56
Disable nf-core linting
code-flowbio Sep 3, 2024
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Update CI action versions
code-flowbio Sep 3, 2024
8110cba
UPdate python version
code-flowbio Sep 3, 2024
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Update nextflow version
code-flowbio Sep 3, 2024
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Add nanopore demux
code-flowbio Sep 3, 2024
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112 changes: 56 additions & 56 deletions .github/workflows/pr_linting.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -25,9 +25,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3
- uses: actions/setup-node@v4

- name: Install Prettier
run: npm install -g prettier
Expand All @@ -42,59 +42,59 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- name: Check code lints with Black
uses: psf/black@stable

nf-core:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3

- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.9.x"

- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Install nf-core
run: python -m pip install --upgrade git+https://github.com/goodwright/tools.git@gw-main

# - name: Restore nf-core packages
# run: nf-core modules list local

- name: Run module linting
run: |
nf-core modules lint dump_software_versions
nf-core modules lint sample/base_samplesheet_check
nf-core modules lint sample/diff_samplesheet_check
nf-core modules lint sample/scmultiome_samplesheet_check
nf-core modules lint ultraplex/samplesheet_to_barcode
nf-core modules lint ultraplex/ultraplex
nf-core modules lint xlsx_to_csv
nf-core modules lint clipseq/filter_gtf
nf-core modules lint clipseq/find_longest_transcript
nf-core modules lint clipseq/resolve_unannotated
nf-core modules lint icount/segment
nf-core modules lint icount/sigxls
nf-core modules lint icount/summary
nf-core modules lint icount/peaks
nf-core modules lint linux/command
nf-core modules lint bedtools/shift
nf-core modules lint clippy
nf-core modules lint paraclu/paraclu
nf-core modules lint paraclu/cut
nf-core modules lint peka
nf-core modules lint samtools/simple_view
nf-core modules lint umicollapse
nf-core modules lint clipseq/clipqc
nf-core modules lint r/deseq2
nf-core modules lint r/deseq2_plots
nf-core modules lint r/pcaexplorer
# nf-core:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v3

# - name: Set up Python
# uses: actions/setup-python@v3
# with:
# python-version: "3.9.x"

# - name: Install Nextflow
# env:
# CAPSULE_LOG: none
# run: |
# wget -qO- get.nextflow.io | bash
# sudo mv nextflow /usr/local/bin/

# - name: Install nf-core
# run: python -m pip install --upgrade git+https://github.com/goodwright/tools.git@gw-main

# # - name: Restore nf-core packages
# # run: nf-core modules list local

# - name: Run module linting
# run: |
# nf-core modules lint dump_software_versions
# nf-core modules lint sample/base_samplesheet_check
# nf-core modules lint sample/diff_samplesheet_check
# nf-core modules lint sample/scmultiome_samplesheet_check
# nf-core modules lint ultraplex/samplesheet_to_barcode
# nf-core modules lint ultraplex/ultraplex
# nf-core modules lint xlsx_to_csv
# nf-core modules lint clipseq/filter_gtf
# nf-core modules lint clipseq/find_longest_transcript
# nf-core modules lint clipseq/resolve_unannotated
# nf-core modules lint icount/segment
# nf-core modules lint icount/sigxls
# nf-core modules lint icount/summary
# nf-core modules lint icount/peaks
# nf-core modules lint linux/command
# nf-core modules lint bedtools/shift
# nf-core modules lint clippy
# nf-core modules lint paraclu/paraclu
# nf-core modules lint paraclu/cut
# nf-core modules lint peka
# nf-core modules lint samtools/simple_view
# nf-core modules lint umicollapse
# nf-core modules lint clipseq/clipqc
# nf-core modules lint r/deseq2
# nf-core modules lint r/deseq2_plots
# nf-core modules lint r/pcaexplorer
22 changes: 11 additions & 11 deletions .github/workflows/unit_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ jobs:
strategy:
fail-fast: false
matrix:
NXF_VER: ["23.04.0", ""]
NXF_VER: ["24.04.4", ""]
profile: ["docker", "singularity"]
tags:
# Modules
Expand Down Expand Up @@ -88,15 +88,15 @@ jobs:
- wrappers/modules/paraclu_paraclu
steps:
- name: Checkout Code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v3
uses: actions/setup-python@v5
with:
python-version: "3.x"
python-version: "3.11"

- name: Setup Pip Cache
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
Expand All @@ -107,7 +107,7 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow

- name: Restore Keys
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
Expand Down Expand Up @@ -171,15 +171,15 @@ jobs:
CAPSULE_LOG: none
steps:
- name: Checkout Code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v3
uses: actions/setup-python@v5
with:
python-version: "3.x"
python-version: "3.11"

- name: Setup Pip Cache
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
Expand All @@ -194,7 +194,7 @@ jobs:
with:
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: "3.9"
python-version: "3.11"

- name: Install Conda dependencies
run: conda install --name test bedtools
Expand Down
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