diff --git a/.travis.yml b/.travis.yml index b200b4a..918a846 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,10 +9,6 @@ cache: pip matrix: fast_finish: true -before_install: - # PRs to master are only ok if coming from dev branch - - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])' - install: # Install Nextflow - mkdir /tmp/nextflow && cd /tmp/nextflow @@ -26,4 +22,8 @@ env: script: # Run the pipeline with the test profile and test remote config - - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | tr -s ' ' | cut -d " " -f 2 | xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {} + - | + grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \ + tr -s ' ' | \ + cut -d " " -f 2 | \ + xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {} diff --git a/README.md b/README.md index 939bf23..6a53642 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,6 @@ Alternatively, instead of using the configuration profiles from this repository, pipeline directly calling the single institutional config file that you need with the `-c` parameter. ```bash -## Example command for nf-core/rnaseq nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config ``` diff --git a/conf/binac.config b/conf/binac.config index cde5218..12da68d 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -5,7 +5,6 @@ params { config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC' } - singularity { enabled = true } @@ -17,7 +16,8 @@ process { } params { - igenomesIgnore = true + igenomesIgnore = false + igenomes_base = '/beegfs/work/igenomes' max_memory = 128.GB max_cpus = 28 max_time = 48.h