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fix: add more logging statemens to sleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass #576

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fix: add more logging statemens to sleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass

fix: add more logging statemens to sleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass #576

Workflow file for this run

.github/workflows/main.yml at 6ea2a0b
#name: My build action requiring more space
#on: push
#
#jobs:
# build:
# name: Build my artifact
# runs-on: ubuntu-latest
# steps:
# - name: Maximize build space
# uses: easimon/maximize-build-space@master
# with:
# root-reserve-mb: 512
# swap-size-mb: 1024
# remove-dotnet: 'true'
# remove-android: 'true'
# remove-haskell: 'true'
# - name: Checkout
# uses: actions/checkout@v2
#
# - name: Build
# run: |
# echo "Free space:"
# df -h
# echo "free space in ${{ github.workspace }}"
# du -hs $(ls -A) ${{ github.workspace }}/*
# rm -rf ${{ github.workspace }}/*
# echo "free space in .test"
# du -hs $(ls -A) .test/*
name: Tests
on:
push:
branches:
- main
pull_request:
branches_ignore: []
jobs:
formatting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Formatting
uses: github/super-linter@v5
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: main
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
VALIDATE_SNAKEMAKE_SNAKEFMT: true
linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Linting
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--lint"
run-rna-workflow:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
submodules: recursive
- name: Test workflow
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp"
run-three-prime-rna-workflow:
runs-on: ubuntu-latest
needs:
- linting
- formatting
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
submodules: recursive
- name: Test 3-prime-workflow
uses: snakemake/snakemake-github-action@v1
with:
directory: .test/three_prime
snakefile: .test/three_prime/workflow/Snakefile
args: "--use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp"
# Disable report testing for now since we mark all output files as temporary above.
# TODO: add some kind of test mode to report generation which does not really try to include
# results.
# - name: Test report
# uses: snakemake/snakemake-github-action@v1
# with:
# directory: .test
# snakefile: workflow/Snakefile
# args: "--report report.zip"