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Update doc related to simpleaf, alevin-fry and salmon. #1031

Update doc related to simpleaf, alevin-fry and salmon.

Update doc related to simpleaf, alevin-fry and salmon. #1031

Workflow file for this run

# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
name: nf-core CI
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
merge_group:
types:
- checks_requested
branches:
- master
- dev
env:
NXF_ANSI_LOG: false
NFT_VER: "0.9.0"
NFT_WORKDIR: "~"
NFT_DIFF: "pdiff"
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}"
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile: ["alevin", "cellranger", "cellrangermulti", "kallisto", "star"]
steps:
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- uses: actions/setup-python@v4
with:
python-version: "3.11"
architecture: "x64"
- name: Install pdiff to see diff between nf-test snapshots
run: |
python -m pip install --upgrade pip
pip install pdiff
- uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- uses: nf-core/setup-nf-test@v1
with:
version: ${{ env.NFT_VER }}
- name: Run nf-test
run: |
nf-test test \
--ci \
--junitxml=test.xml \
tests/main_pipeline_${{ matrix.profile }}.nf.test
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: test.xml