diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 3936468..66bf36b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -49,6 +49,7 @@ jobs: - "cfc_dev" - "cheaha" - "computerome" + - "crg" - "crick" - "crukmi" - "denbi_qbic" diff --git a/README.md b/README.md index fe38eb9..a066053 100644 --- a/README.md +++ b/README.md @@ -228,6 +228,8 @@ Currently documentation is available for the following pipelines within specific - taxprofiler - [EVA](docs/pipeline/taxprofiler/eva.md) - [hasta](docs/pipeline/taxprofiler/hasta.md) +- proteinfold + - [CRG](docs/pipeline/proteinfold/crg.md) ### Pipeline-specific documentation diff --git a/conf/crg.config b/conf/crg.config new file mode 100755 index 0000000..7216b80 --- /dev/null +++ b/conf/crg.config @@ -0,0 +1,14 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'Centre for Genomic Regulation (CRG) cluster profile provided by nf-core/configs' + config_profile_contact = 'Athanasios Baltzis (@athbaltzis)' + config_profile_url = 'http://www.linux.crg.es/index.php/Main_Page' +} + +process { + executor = 'crg' +} + +singularity { + enabled = true +} diff --git a/conf/pipeline/proteinfold/crg.config b/conf/pipeline/proteinfold/crg.config new file mode 100644 index 0000000..f778d8c --- /dev/null +++ b/conf/pipeline/proteinfold/crg.config @@ -0,0 +1,27 @@ +profiles { + crg { + params { + config_profile_contact = 'Athanasios Baltzis (@athbaltzis)' + config_profile_description = 'nf-core/proteinfold CRG profile provided by nf-core/configs' + } + executor.name = 'crg' + process { + queue = 'short-sl7,long-sl7' + withName: 'RUN_AF2|RUN_AF2_PRED|COLABFOLD_BATCH' { + cpus = 1 + memory = "30 GB" + queue = params.use_gpu ? 'gpu' : 'long-sl7' + clusterOptions = { ( task.queue == 'gpu' ? '-l gpu=1' : '' ) } + } + withName: 'ARIA2' { + time = '12h' + } + withName: 'MMSEQS_COLABFOLDSEARCH' { + queue = 'mem_512' + memory = "100 GB" + cpus = 8 + time = '12h' + } + } + } +} diff --git a/docs/pipeline/proteinfold/crg.md b/docs/pipeline/proteinfold/crg.md new file mode 100644 index 0000000..9b11d2a --- /dev/null +++ b/docs/pipeline/proteinfold/crg.md @@ -0,0 +1,23 @@ +# nf-core/configs: CRG proteinfold specific configuration + +Extra specific configuration for proteinfold pipeline + +## Usage + +To use, run the pipeline with `-profile crg`. + +This will download and launch the proteinfold specific [`crg.config`](../../../conf/pipeline/proteinfold/crg.config) which has been pre-configured with a setup suitable for the sge cluster. + +Example: `nextflow run nf-core/proteinfold -profile crg` + +## proteinfold specific configurations for CRG + +Specific configurations for CRG has been made for proteinfold. + +### General profiles + + + +### Contextual profiles + + diff --git a/nfcore_custom.config b/nfcore_custom.config index 51c1121..53d7682 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -30,6 +30,7 @@ profiles { cfc_dev { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" } cheaha { includeConfig "${params.custom_config_base}/conf/cheaha.config" } computerome { includeConfig "${params.custom_config_base}/conf/computerome.config" } + crg { includeConfig "${params.custom_config_base}/conf/crg.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } crukmi { includeConfig "${params.custom_config_base}/conf/crukmi.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } diff --git a/pipeline/proteinfold.config b/pipeline/proteinfold.config new file mode 100644 index 0000000..e4f59b4 --- /dev/null +++ b/pipeline/proteinfold.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------- + * nfcore/proteinfold custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/proteinfold folder and imported + * under a profile name here. + */ + +profiles { + crg { includeConfig "${params.custom_config_base}/conf/pipeline/proteinfold/crg.config" } +}