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Merge pull request #60 from drpatelh/master

Attempt to get travis tests working
This commit is contained in:
Harshil Patel 2019-08-01 13:46:44 +01:00 committed by GitHub
commit 5abe8bca35
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4 changed files with 14 additions and 14 deletions

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@ -17,8 +17,8 @@ install:
- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
env:
- NXF_VER='18.10.1' # Specify a minimum NF version that should be tested and work
- NXF_VER='' # Plus: get the latest NF version and check, that it works
- NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
- NXF_VER='' SCRATCH='~' # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.
script:
# Run the pipeline with the test profile and test remote config
@ -26,4 +26,5 @@ script:
grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
tr -s ' ' | \
cut -d " " -f 2 | \
grep -v "czbiohub_aws" | \
xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}

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@ -82,24 +82,26 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following clusters:
* [BINAC](docs/binac.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md)
* [CCGA](docs/ccga.md)
* [CCGA_DX](/docs/ccga_dx.md)
* [CFC](docs/binac.md)
* [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md)
* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
* [GIS](docs/gis.md)
* [HEBBE](docs/hebbe.md)
* [MENDEL](docs/mendel.md)
* [MUNIN](docs/munin.md)
* [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md)
* [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md)
* [UPPMAX-DEVEL](docs/uppmax-devel.md)
* [UPPMAX](docs/uppmax.md)
* [UPPMAX_DEVEL](docs/uppmax.md)
* [UZH](docs/uzh.md)
* [PASTEUR](docs/pasteur.md)
### Uploading to `nf-core/configs`
@ -111,4 +113,4 @@ We will be notified automatically when you have created your pull request, and p
## Help
If you have any questions or issues please send us a message on [Slack](https://nf-core-invite.herokuapp.com/).
If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).

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@ -12,29 +12,26 @@ params.custom_config_version = 'master'
params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
profiles {
bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
czbiohub_aws_highpriority {
includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"
includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"
}
czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
mendel { includeConfig "${params.custom_config_base}/conf/mendel.config" }
munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
}
// If user hostnames contain one of these substring and they are