millironx/nf-configs
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Merge pull request #94 from apeltzer/master

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Mini Cosmetic Fixes for README
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Alexander Peltzer 2019-11-26 16:24:30 +01:00 committed by GitHub
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7
README.md
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@ -1,12 +1,11 @@
# [![nf-core/configs](docs/images/nfcore-configs_logo.png)](https://github.com/nf-core/configs) # [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs)
[![Lint Status](https://github.com/nf-core/configs/workflows/nfcore%20configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/nfcore%20configs%20tests/badge.svg) [![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)
A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions. A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
## Table of contents ## Table of contents
* [![nf-core/configs](https://github.com/nf-core/configs)](#nf-coreconfigshttpsgithubcomnf-coreconfigs)
* [Table of contents](#table-of-contents) * [Table of contents](#table-of-contents)
* [Using an existing config](#using-an-existing-config) * [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters) * [Configuration and parameters](#configuration-and-parameters)
@ -116,7 +115,7 @@ Currently documentation is available for the following systems:
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone. [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that.
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information. Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.

2
bin/cchecker.py
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@ -64,7 +64,7 @@ def check_config(Config, Github):
sys.exit(0) sys.exit(0)
else: else:
#Maybe report what is missing here too #Maybe report what is missing here too
print("Tests don't seem to test these profiles properly!\n") print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n")
print(config_profiles.symmetric_difference(tests)) print(config_profiles.symmetric_difference(tests))
sys.exit(1) sys.exit(1)

1
conf/genotoul.config
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@ -19,6 +19,7 @@ process {
params { params {
save_reference = true save_reference = true
igenomes_ignore = true igenomes_ignore = true
igenomesIgnore = true //deprecated
// Max resources requested by a normal node on genotoul. // Max resources requested by a normal node on genotoul.
max_memory = 120.GB max_memory = 120.GB
max_cpus = 48 max_cpus = 48