mirror of
https://github.com/MillironX/nf-configs.git
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Merge pull request #60 from drpatelh/master
Attempt to get travis tests working
This commit is contained in:
commit
5abe8bca35
4 changed files with 14 additions and 14 deletions
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@ -17,8 +17,8 @@ install:
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- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
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env:
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- NXF_VER='18.10.1' # Specify a minimum NF version that should be tested and work
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- NXF_VER='' # Plus: get the latest NF version and check, that it works
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- NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
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- NXF_VER='' SCRATCH='~' # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.
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script:
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# Run the pipeline with the test profile and test remote config
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@ -26,4 +26,5 @@ script:
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grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
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tr -s ' ' | \
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cut -d " " -f 2 | \
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grep -v "czbiohub_aws" | \
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xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
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10
README.md
10
README.md
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@ -82,24 +82,26 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
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Currently documentation is available for the following clusters:
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* [BINAC](docs/binac.md)
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* [BIGPURPLE](docs/bigpurple.md)
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* [BINAC](docs/binac.md)
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* [CCGA](docs/ccga.md)
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* [CCGA_DX](/docs/ccga_dx.md)
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* [CFC](docs/binac.md)
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* [CRICK](docs/crick.md)
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* [CZBIOHUB_AWS](docs/czbiohub.md)
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* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
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* [GIS](docs/gis.md)
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* [HEBBE](docs/hebbe.md)
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* [MENDEL](docs/mendel.md)
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* [MUNIN](docs/munin.md)
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* [PASTEUR](docs/pasteur.md)
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* [PHOENIX](docs/phoenix.md)
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* [PRINCE](docs/prince.md)
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* [SHH](docs/shh.md)
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* [UCT_HEX](docs/uct_hex.md)
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* [UPPMAX-DEVEL](docs/uppmax-devel.md)
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* [UPPMAX](docs/uppmax.md)
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* [UPPMAX_DEVEL](docs/uppmax.md)
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* [UZH](docs/uzh.md)
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* [PASTEUR](docs/pasteur.md)
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### Uploading to `nf-core/configs`
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@ -111,4 +113,4 @@ We will be notified automatically when you have created your pull request, and p
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## Help
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If you have any questions or issues please send us a message on [Slack](https://nf-core-invite.herokuapp.com/).
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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'
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params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
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profiles {
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bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
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binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
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ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
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ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
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cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
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crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
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czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
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czbiohub_aws_highpriority {
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"
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includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"
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}
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czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
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mendel { includeConfig "${params.custom_config_base}/conf/mendel.config" }
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munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
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pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
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phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
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prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
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shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
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uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
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uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
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uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
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uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
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uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
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prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
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bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
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pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
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}
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// If user hostnames contain one of these substring and they are
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