Commit 92cff2bb authored by Sander Bollen's avatar Sander Bollen
Browse files

small fixes

parent 3c8b10f4
Pipeline #2589 failed with stages
in 3 minutes and 46 seconds
...@@ -34,6 +34,7 @@ test_dry_run: ...@@ -34,6 +34,7 @@ test_dry_run:
test_integration_singularity: test_integration_singularity:
before_script: before_script:
- apt-get update && apt-get install -y python3-pip - apt-get update && apt-get install -y python3-pip
- pip3 install pyfaidx
- pip3 install -r requirements-dev.txt - pip3 install -r requirements-dev.txt
script: script:
- py.test --tag singularity-integration - py.test --tag singularity-integration
......
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
- name: test-singularity-integration-no-cluster - name: test-singularity-integration-no-cluster
command: >- command: >-
bash -c ' bash -c '
snakemake --singularity --jobs 100 -w 120 snakemake --use-singularity --jobs 100 -w 120
-r -p -s Snakefile -r -p -s Snakefile
--config REFERENCE=tests/data/ref.fa GATK=tests/data/ref.fa --config REFERENCE=tests/data/ref.fa GATK=tests/data/ref.fa
DBSNP=tests/data/database.vcf.gz DBSNP=tests/data/database.vcf.gz
......
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