From 71bc98afaef852562d5664d7861cc31cb870db79 Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Mon, 29 Jul 2019 12:06:29 +0200 Subject: [PATCH 1/4] Adding config file for CCGA dx cluster --- docs/ccga_dx.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/ccga_dx.md diff --git a/docs/ccga_dx.md b/docs/ccga_dx.md new file mode 100644 index 0000000..62bf29c --- /dev/null +++ b/docs/ccga_dx.md @@ -0,0 +1,9 @@ +# nf-core/configs: CCGA DX Configuration + +Deployment and testing of nf-core pipelines at the CCGA DX cluster is on-going. + +To use, run the pipeline with `-profile ccga_dx`. This will download and launch the [`ccga.config`](../conf/ccga.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 have Nextflow installed. + +>NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner). From b31db18dfb0b790aecc81c3685a5cc30a57fccec Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Mon, 29 Jul 2019 12:08:07 +0200 Subject: [PATCH 2/4] Adding config file for CCGA dx cluster --- README.md | 1 + conf/ccga_dx.config | 37 +++++++++++++++++++++++++++++++++++++ nfcore_custom.config | 1 + 3 files changed, 39 insertions(+) create mode 100644 conf/ccga_dx.config diff --git a/README.md b/README.md index 73b01be..d865c89 100644 --- a/README.md +++ b/README.md @@ -85,6 +85,7 @@ Currently documentation is available for the following clusters: * [BINAC](docs/binac.md) * [BIGPURPLE](docs/bigpurple.md) * [CCGA](docs/ccga.md) +* [CCGA-DX]/docs/ccga_dx.md) * [CFC](docs/binac.md) * [CRICK](docs/crick.md) * [GIS](docs/gis.md) diff --git a/conf/ccga_dx.config b/conf/ccga_dx.config new file mode 100644 index 0000000..0af95e7 --- /dev/null +++ b/conf/ccga_dx.config @@ -0,0 +1,37 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'CCGA DX 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 +} + +executor { + queueSize=100 +} + +process { + + // Global process config + executor = 'slurm' + queue = 'htc' + +} + +params { + // illumina iGenomes reference file paths on DX Cluster + igenomes_base = '/mnt/ld_ng_out/sukmb352/references/iGenomes/references/' + saveReference = true + max_memory = 250.GB + max_cpus = 20 + max_time = 240.h +} diff --git a/nfcore_custom.config b/nfcore_custom.config index 41b0ade..d4ae35b 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -14,6 +14,7 @@ params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/$ profiles { 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" } From 7d5de651aa238c77f6bee3347622d34c1aa8a942 Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Mon, 29 Jul 2019 12:45:08 +0200 Subject: [PATCH 3/4] Update README.md Co-Authored-By: Harshil Patel --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d865c89..d7b43fb 100644 --- a/README.md +++ b/README.md @@ -85,7 +85,7 @@ Currently documentation is available for the following clusters: * [BINAC](docs/binac.md) * [BIGPURPLE](docs/bigpurple.md) * [CCGA](docs/ccga.md) -* [CCGA-DX]/docs/ccga_dx.md) +* [CCGA_DX](/docs/ccga_dx.md) * [CFC](docs/binac.md) * [CRICK](docs/crick.md) * [GIS](docs/gis.md) From b74f020f14d3254d67d85edaa2a3c8d20dfea389 Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Mon, 29 Jul 2019 12:45:30 +0200 Subject: [PATCH 4/4] Update docs/ccga_dx.md Co-Authored-By: Harshil Patel --- docs/ccga_dx.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ccga_dx.md b/docs/ccga_dx.md index 62bf29c..0cea81e 100644 --- a/docs/ccga_dx.md +++ b/docs/ccga_dx.md @@ -2,7 +2,7 @@ Deployment and testing of nf-core pipelines at the CCGA DX cluster is on-going. -To use, run the pipeline with `-profile ccga_dx`. This will download and launch the [`ccga.config`](../conf/ccga.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. +To use, run the pipeline with `-profile ccga_dx`. This will download and launch the [`ccga_dx.config`](../conf/ccga_dx.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 have Nextflow installed.