Merge pull request #24 from nf-core/dev

Dev

docs/usage.md

@@ -371,6 +371,26 @@ Provide git commit id for custom Institutional configs hosted at `nf-core/config
 --custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
 ```
 
+### `--custom_config_base`
+If you're running offline, nextflow will not be able to fetch the institutional config files
+from the internet. If you don't need them, then this is not a problem. If you do need them,
+you should download the files from the repo and tell nextflow where to find them with the
+`custom_config_base` option. For example:
+
+```bash
+## Download and unzip the config files
+cd /path/to/my/configs
+wget https://github.com/nf-core/configs/archive/master.zip
+unzip master.zip
+
+## Run the pipeline
+cd /path/to/my/data
+nextflow run /path/to/atacseq_pipeline/ --custom_config_base /path/to/my/configs/configs-master/
+```
+
+> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
+> files + singularity containers + institutional configs in one go for you, to make this process easier.
+
 ### `--max_memory`
 Use to set a top-limit for the default memory requirement for each process.
 Should be a string in the format integer-unit. eg. `--max_memory '8.GB'`

nextflow.config

@@ -65,14 +65,19 @@ params {
   clusterOptions = false
   igenomesIgnore = false
   custom_config_version = 'master'
+  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
 
 }
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
 // Load nf-core custom profiles from different Institutions
-includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config"
+try {
+  includeConfig "${params.custom_config_base}/nfcore_custom.config"
+} catch (Exception e) {
+  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
+}
 
 profiles {
   awsbatch { includeConfig 'conf/awsbatch.config' }