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Moved custom Institutional configs to nf-core configs on github #212

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Merged
apeltzer merged 1 commit into from
Nov 26, 2018
+23 −27
Merged

Moved custom Institutional configs to nf-core configs on github #212

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8 changes: 8 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,13 @@
# nf-core/tools: Changelog

## v1.3dev
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@apeltzer apeltzer Nov 26, 2018

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Suggested change
## v1.3dev
## v1.4dev

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@drpatelh drpatelh Nov 26, 2018

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Sorry. Thats exactly what I meant!

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@drpatelh drpatelh Nov 26, 2018

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How do you make these changes after merging @apeltzer? My naive brain is trying to work it out!

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@apeltzer apeltzer Nov 26, 2018

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My bad - I've merged before really thinking as I thought the commit was fine and good (expect for these smallish typos). I guess just make a new PR with just these two then and I'll merge it in... sorry about that.

Normally you can simply click "accept" and thats it... :-)

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@drpatelh drpatelh Nov 26, 2018

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No worries. I have fixed this in #214 whilst I was dealing with another issue.

* Institutional custom config profiles moved to github `nf-core/configs`
* These will now be maintained centrally as opposed to being shipped with the pipelines in `conf/`
* Load `base.config` by default for all profiles
* Removed profiles named `standard` and `none`
* Added parameter `--igenomesIgnore` so `igenomes.config` isnt loaded if parameter clashes are observed
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@apeltzer apeltzer Nov 26, 2018

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Suggested change
* Added parameter `--igenomesIgnore` so `igenomes.config` isnt loaded if parameter clashes are observed
* Added parameter `--igenomesIgnore` so `igenomes.config` isn't loaded if parameter clashes are observed

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@drpatelh drpatelh Nov 26, 2018

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Agreed!

* Added parameter `--custom_config_version` for custom config version control. Can use this parameter to provide commit id for reproducibility. Defaults to `master`

##[v1.3](https://github.com/nf-core/tools/releases/tag/1.3) - 2018-11-21
* `nf-core create` command line interface updated
* Interactive prompts for required arguments if not given
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42 changes: 15 additions & 27 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
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Expand Up @@ -32,46 +32,34 @@ params {
clusterOptions = false
awsqueue = false
awsregion = 'eu-west-1'
igenomesIgnore = false
custom_config_version = 'master'
}

// 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"

profiles {
awsbatch {
includeConfig 'conf/base.config'
includeConfig 'conf/awsbatch.config'
includeConfig 'conf/igenomes.config'
}
binac {
includeConfig 'conf/base.config'
includeConfig 'conf/binac.config'
}
cfc {
includeConfig 'conf/base.config'
includeConfig 'conf/cfc.config'
}
awsbatch { includeConfig 'conf/awsbatch.config' }
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
process.container = params.container
}
none {
// Don't load any config (for use with custom home configs)
}
singularity {
singularity.enabled = true
process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
}
standard {
includeConfig 'conf/base.config'
}
test {
includeConfig 'conf/base.config'
includeConfig 'conf/test.config'
}
uzh {
includeConfig 'conf/base.config'
includeConfig 'conf/uzh.config'
}
test { includeConfig 'conf/test.config' }
}

// Load igenomes.config if required
if(!params.igenomesIgnore){
includeConfig 'conf/igenomes.config'
}

// Capture exit codes from upstream processes when piping
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