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sdrfToNfConf_test.yml
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name: R script check
on:
push:
branches:
- develop
pull_request:
branches:
- develop
jobs:
run_script:
runs-on: ubuntu-latest
steps:
- name: checkout code
uses: actions/checkout@v3
- name: set up R
uses: r-lib/actions/setup-r@v2
with:
r-version: 3.6.3
- name: install devtools related dependencies
run: sudo apt install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libcurl4-openssl-dev libbz2-dev liblzma-dev
- name: install dependencies
run: |
Rscript -e 'install.packages(c("data.table", "optparse", "devtools"))'
Rscript -e 'devtools::install_github("ebi-gene-expression-group/workflow-scripts-common")'
- name: run test
run: |
set -e
out_test1=$(pwd)/test1
Rscript bin/sdrfToNfConf.R --sdrf=tests/E-MTAB-4850.homo_sapiens.sdrf.txt --idf=tests/E-MTAB-4850.homo_sapiens.idf.txt --name=E-MTAB-4850 --verbose --out_conf $out_test1
- name: check for errors
run: Rscript -e 'stopifnot(identical(geterrmessage(), ""))'