diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 45fe4bb..019a3ee 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow @@ -24,7 +24,7 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - name: Check ${{ matrix.profile }} profile - env: + env: SCRATCH: '~' NXF_GLOBAL_CONFIG: awsbatch.config run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} diff --git a/README.md b/README.md index 7da6090..5ac8a6e 100644 --- a/README.md +++ b/README.md @@ -117,7 +117,7 @@ Currently documentation is available for the following systems: * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) * [SHH](docs/shh.md) -* [UCT_HEX](docs/uct_hex.md) +* [UCT_HPC](docs/uct_hpc.md) * [UPPMAX](docs/uppmax.md) * [UTD_GANYMEDE](docs/utd_ganymede.md) * [UZH](docs/uzh.md) diff --git a/conf/uct_hex.config b/conf/uct_hex.config deleted file mode 100644 index 6e0bbbe..0000000 --- a/conf/uct_hex.config +++ /dev/null @@ -1,23 +0,0 @@ -//Profile config names for nf-core/configs -params { - config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.' - config_profile_contact = 'Katie Lennard (@kviljoen)' - config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/' -} - -singularity { - enabled = true - cacheDir = "/scratch/DB/bio/singularity-containers" -} - -process { - stageInMode = 'symlink' - stageOutMode = 'rsync' - queue = 'UCTlong' - clusterOptions = { "-M $params.email -m abe -l nodes=1:ppn=1:series600" } -} - -executor{ - executor = 'pbs' - jobName = { "$task.tag" } -} diff --git a/conf/uct_hpc.config b/conf/uct_hpc.config new file mode 100644 index 0000000..e7218ba --- /dev/null +++ b/conf/uct_hpc.config @@ -0,0 +1,41 @@ +/* + * ------------------------------------------------- + * HPC cluster config file + * ------------------------------------------------- + * http://www.hpc.uct.ac.za/ + */ + +params { + config_profile_description = 'University of Cape Town High Performance Cluster config file provided by nf-core/configs.' + config_profile_contact = 'Katie Lennard (@kviljoen)' + config_profile_url = 'http://hpc.uct.ac.za/index.php/hpc-cluster/' + + singularity_cache_dir = "/bb/DB/bio/singularity-containers/" + igenomes_base = '/bb/DB/bio/rna-seq/references' + max_memory = 384.GB + max_cpus = 40 + max_time = 1000.h + hpc_queue = 'ada' + hpc_account = '--account cbio' + genome = 'GRCh37' +} + +singularity { + enabled = true + cacheDir = params.singularity_cache_dir + autoMounts = true +} + +process { + executor = 'slurm' + queue = params.hpc_queue + // Increasing maxRetries, this will overwrite what we have in base.config + maxRetries = 4 + clusterOptions = params.hpc_account + stageInMode = 'symlink' + stageOutMode = 'rsync' +} + +executor { + queueSize = 15 +} diff --git a/docs/uct_hpc.md b/docs/uct_hpc.md new file mode 100644 index 0000000..dd24e3f --- /dev/null +++ b/docs/uct_hpc.md @@ -0,0 +1,5 @@ +# nf-core/configs: UCT HPC config + +University of Cape Town [High Performance Cluster](http://hpc.uct.ac.za/index.php/hpc-cluster/) config. + +For help or more information, please contact Katie Lennard (@kviljoen). diff --git a/nfcore_custom.config b/nfcore_custom.config index aa084dc..c856521 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -35,7 +35,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } - uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } + uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uppmax { includeConfig "${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" }