Merge pull request #60 from drpatelh/master

Attempt to get travis tests working

.travis.yml

@@ -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='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
-  - NXF_VER='' # Plus: get the latest NF version and check, that it works
+  - 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 {}

README.md

@@ -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).

nfcore_custom.config

@@ -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 "${params.custom_config_base}/conf/czbiohub_aws.config" }
-  czbiohub_aws_highpriority {
+  czbiohub_aws_highpriority { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config"; includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config" }
-    includeConfig "${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