Skip to content
Snippets Groups Projects
Commit 0411ae5d authored by MihaelaZavolan's avatar MihaelaZavolan
Browse files

Added nextflow installation test

parent 95d07fbd
No related branches found
No related tags found
1 merge request!11Wrapper
Pipeline #13610 failed
...@@ -11,7 +11,7 @@ qc_1: ...@@ -11,7 +11,7 @@ qc_1:
- pip install -r requirements.txt - pip install -r requirements.txt
- pip install -r requirements_dev.txt - pip install -r requirements_dev.txt
- pip install -e . - pip install -e .
script: script:
- flake8 src/ setup.py - flake8 src/ setup.py
- coverage run --source src/ -m pytest - coverage run --source src/ -m pytest
...@@ -25,7 +25,11 @@ test_1: ...@@ -25,7 +25,11 @@ test_1:
- pip install -r requirements.txt - pip install -r requirements.txt
- pip install -r requirements_dev.txt - pip install -r requirements_dev.txt
- pip install -e . - pip install -e .
- apt update -y
- apt install wget -y
- wget -qO- https://get.nextflow.io | bash
- nextflow self-update
script: script:
- python -m pytest - nextflow main.nf
main.nf 0 → 100755
/*
* pipeline input parameters
*/
params.annoFile = "$baseDir/inputs/ref_annotation.gt"
params.copyNr = "$baseDir/inputs/transcript_tpms.txt"
params.outdir = "results"
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
annotation : ${params.annoFile}
copy numbers: ${params.copyNr}
output dir : ${params.outdir}
"""
.stripIndent()
/*
* check that input files are there
*/
process mock {
input:
path annoFile from params.annoFile
path copyNr from params.copyNr
script:
"""
echo "Checked $annoFile and $copyNr"
"""
}
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment