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Try separating MALT

This commit is contained in:
James Fellows Yates 2022-12-04 12:06:33 +01:00
parent 0dccfddc24
commit 0a0dffa37c
2 changed files with 34 additions and 1 deletions

View file

@ -134,3 +134,36 @@ jobs:
with:
command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
attempt_limit: 3
malt:
name: Test MALT with workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "21.10.3"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Show current locale
run: locale
- name: Set UTF-8 enabled locale
run: |
sudo locale-gen en_US.UTF-8
sudo update-locale LANG=en_US.UTF-8
- name: Run pipeline with test data
uses: Wandalen/wretry.action@v1.0.11
with:
command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --outdir ./results
attempt_limit: 3

View file

@ -35,7 +35,7 @@ params {
run_kaiju = true
run_kraken2 = true
run_bracken = true
run_malt = true
run_malt = false
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true