From af1e57027d17dd09c416ae94c7e5dbb2db1f0e2b Mon Sep 17 00:00:00 2001 From: ikeller Date: Wed, 19 May 2021 09:46:07 +0200 Subject: [PATCH] edit config and readme --- .github/workflows/main.yml | 2 +- README.md | 1 + conf/unibe_ibu.config | 23 +++++++++++++++++++++++ docs/unibe_ibu.md | 8 ++++++++ nfcore_custom.config | 1 + 5 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 docs/unibe_ibu.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 65cabe5..25a583b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'unibe_ibu', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 6daff2a..2d0ca9f 100644 --- a/README.md +++ b/README.md @@ -128,6 +128,7 @@ Currently documentation is available for the following systems: * [SEG_GLOBE](docs/seg_globe.md) * [SHH](docs/shh.md) * [UCT_HPC](docs/uct_hpc.md) +* [UNIBE_IBU](docs/unibe_ibu.md) * [UPPMAX](docs/uppmax.md) * [UTD_GANYMEDE](docs/utd_ganymede.md) * [UZH](docs/uzh.md) diff --git a/conf/unibe_ibu.config b/conf/unibe_ibu.config index e69de29..cda6ace 100644 --- a/conf/unibe_ibu.config +++ b/conf/unibe_ibu.config @@ -0,0 +1,23 @@ +params { + config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile" + config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch" + config_profile_url = "https://www.bioinformatics.unibe.ch/" + max_memory = 500.GB + max_cpus = 128 + max_time = 28.d +} + +process { + executor = "slurm" + maxRetries = 2 + beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/' +} + +executor { + queueSize = 30 +} + +singularity { + enable = true + autoMounts = true +} \ No newline at end of file diff --git a/docs/unibe_ibu.md b/docs/unibe_ibu.md new file mode 100644 index 0000000..8070dc5 --- /dev/null +++ b/docs/unibe_ibu.md @@ -0,0 +1,8 @@ +# nf-core/configs: UNIBE_IBU Configuration + +Configuration file to run nf-core pipelines on the cluster of the [Interfaculty Bioinformatics Unit](https://www.bioinformatics.unibe.ch/) of the University of Bern. + +To use, run the pipeline with `-profile unibe_ibu`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU 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. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. + + + diff --git a/nfcore_custom.config b/nfcore_custom.config index 9b4fbda..8781322 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -47,6 +47,7 @@ profiles { seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } + unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }