From 0830203b705f21e0998219255a3a9fc37162dd6a Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Fri, 7 Feb 2020 11:09:22 +0100 Subject: [PATCH 1/6] Adding new CCGA Med Cluster to profiles Updating README and fixing linting errors in CCGA_MED profile Fixing order in profile queue and removed leading slash from readme for ccga profile docs Fixing order in profile queue and removed leading slash from readme for ccga profile docs --- .github/workflows/main.yml | 2 +- README.md | 11 +++++++++-- conf/ccga_med.config | 39 ++++++++++++++++++++++++++++++++++++++ docs/ccga_med.md | 16 ++++++++++++++++ nfcore_custom.config | 1 + 5 files changed, 66 insertions(+), 3 deletions(-) create mode 100644 conf/ccga_med.config create mode 100644 docs/ccga_med.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 43c15cf..5fb2601 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 7f2665e..19d40f6 100644 --- a/README.md +++ b/README.md @@ -99,7 +99,8 @@ Currently documentation is available for the following systems: * [BINAC](docs/binac.md) * [CBE](docs/cbe.md) * [CCGA](docs/ccga.md) -* [CCGA_DX](/docs/ccga_dx.md) +* [CCGA_DX](docs/ccga_dx.md) +* [CCGA_MED](docs/ccga_med.md) * [CFC](docs/binac.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) @@ -126,7 +127,13 @@ Within the local clone of your fork add the custom config file to the [`conf/`]( 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. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) 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 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. +In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error: +```bash +Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml +Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML. +set(['']) +##[error]Process completed with exit code 1. +``` 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. diff --git a/conf/ccga_med.config b/conf/ccga_med.config new file mode 100644 index 0000000..d55fde2 --- /dev/null +++ b/conf/ccga_med.config @@ -0,0 +1,39 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'CCGA Med cluster profile provided by nf-core/configs.' + config_profile_contact = 'Marc Hoeppner (@marchoeppner)' + config_profile_url = 'https://www.ccga.uni-kiel.de/' +} + +/* + * ------------------------------------------------- + * Nextflow config file for CCGA cluster in Kiel + * ------------------------------------------------- + */ + +singularity { + enabled = true + runOptions = "-B /work_ifs -B /scratch" + cacheDir = "/work_ifs/ikmb_repository/singularity_cache/" +} + +executor { + queueSize=100 +} + +process { + + // Global process config + executor = 'slurm' + queue = 'all' + +} + +params { + // illumina iGenomes reference file paths on RZCluster + igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/' + saveReference = true + max_memory = 250.GB + max_cpus = 24 + max_time = 120.h +} diff --git a/docs/ccga_med.md b/docs/ccga_med.md new file mode 100644 index 0000000..9aa4236 --- /dev/null +++ b/docs/ccga_med.md @@ -0,0 +1,16 @@ +# nf-core/configs: CCGA Med Cluster Configuration + +Deployment and testing of nf-core pipelines at the CCGA Med cluster is on-going. + +To use, run the pipeline with `-profile ccga_med`. This will download and launch the [`ccga_med.config`](../conf/ccga_med.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load nextflow +module load singularity +``` + +>NB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner). diff --git a/nfcore_custom.config b/nfcore_custom.config index 404d11e..8b4a3a9 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -19,6 +19,7 @@ profiles { cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } + ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } cfc { includeConfig "${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" } From ef8534d481a569ac55283faf6b1baf515d6feb66 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 11 Feb 2020 11:57:04 +0000 Subject: [PATCH 2/6] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 19d40f6..3011a00 100644 --- a/README.md +++ b/README.md @@ -128,6 +128,7 @@ You will also need to edit and add your custom profile to the [`nfcore_custom.co You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error: + ```bash Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML. 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zXL)g3;1F*m&)K}O@4Y083FNm~xDtui)E3(s5!e#3nT20}XI5x^6<_}ycOKeX#@OyV zK + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + Config files used to define parameters specific tocompute environments at different Institutions + configs + + + + + + + + + + + + + + + + + + + + + + + + + From 744db30da4a5d9a96229fbf26a7c6b749a2dc4b0 Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Wed, 19 Feb 2020 11:27:02 +0100 Subject: [PATCH 4/6] Update binac.config This is now close to optimal I think. --- conf/binac.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index 21f2459..d3624df 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -13,14 +13,14 @@ singularity { process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'pbs' - queue = { task.memory >= 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time <= 48.h ? 'short' : task.time <= 168.h ? 'short' : 'long'} + queue = { task.memory >= 128.GB ? 'smp': task.time <= 20.m ? 'tiny' : task.time > 48.h ? 'long' : 'short'} } params { igenomes_base = '/nfsmounts/igenomes' max_memory = 1000.GB max_cpus = 28 - max_time = 48.h + max_time = 168.h } weblog{ From 2144a1dc04ac5c8756c60ae053eed95e149ecfa7 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 20 Feb 2020 17:19:30 +0100 Subject: [PATCH 5/6] Apply suggestions from code review --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4d2f8bd..0e58b09 100644 --- a/README.md +++ b/README.md @@ -196,7 +196,7 @@ We will be notified automatically when you have created your pull request, and p [Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account. And add or edit the following files in the local clone of your fork. -- `pipeline/.config` +* `pipeline/.config` If not already created, create the `pipeline/.config` file, and add your custom profile to the profile scope From 9b897345da7cbffbd80f61337f3edad2aea70735 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Fri, 21 Feb 2020 08:16:31 +0100 Subject: [PATCH 6/6] Update conf/pipeline/sarek/uppmax.config Co-Authored-By: Phil Ewels --- conf/pipeline/sarek/uppmax.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/pipeline/sarek/uppmax.config b/conf/pipeline/sarek/uppmax.config index 4a1a9fa..4690f9e 100644 --- a/conf/pipeline/sarek/uppmax.config +++ b/conf/pipeline/sarek/uppmax.config @@ -7,7 +7,7 @@ params { if (hostname ==~ "i.*") { singularity { - cacheDir = "${params.containers_path}" + cacheDir = params.containers_path } }