diff --git a/README.md b/README.md index 112dc021d..6035d4f44 100644 --- a/README.md +++ b/README.md @@ -255,6 +255,8 @@ Currently documentation is available for the following pipelines within specific - ampliseq - [BINAC](docs/pipeline/ampliseq/binac.md) - [UPPMAX](docs/pipeline/ampliseq/uppmax.md) +- cutandrun + - [UNC_LONGLEAF](docs/pipeline/cutandrun/unc_longleaf.md) - demultiplex - [AWS_TOWER](docs/pipeline/demultiplex/aws_tower.md) - eager diff --git a/docs/pipeline/cutandrun/unc_longleaf.md b/docs/pipeline/cutandrun/unc_longleaf.md new file mode 100644 index 000000000..2b8f6e860 --- /dev/null +++ b/docs/pipeline/cutandrun/unc_longleaf.md @@ -0,0 +1,22 @@ +# nf-core/configs: UNC's Longleaf CUT&RUN specific configuration + +Extra specific configuration for eager pipeline + +## Pipeline specific profiles + +Specific-pipeline profiles exist for the following pipelines, and will be automatically loaded when supplying `-profile unc_longleaf` to your command: + +- cutandrun + +## Usage + +To use, run the pipeline with `-profile unc_longleaf`. + +This will download and launch the eager specific [`unc_longleaf.config`](../../../conf/pipeline/cutandrun/unc_longleaf.config) which is adapted to data generated at UNC-CH and +processed on the Longleaf HPC. + +Example: `nextflow run nf-core/cutandrun -profile unc_longleaf` + +### Specifics + +This custom config adds extra memory to the FRAG_LEN_HIST and DEEPTOOLS_PLOTHEATMAP_GENE_ALL as the jobs kept failing with default memory limits diff --git a/pipeline/cutandrun.config b/pipeline/cutandrun.config new file mode 100644 index 000000000..126e506c0 --- /dev/null +++ b/pipeline/cutandrun.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------------ + * nfcore/cutandrun custom profile Nextflow config file + * ------------------------------------------------------ + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/cutandrun folder and imported + * under a profile name here. + */ + +profiles { + unc_longleaf { includeConfig "${params.custom_config_base}/conf/pipeline/cutandrun/unc_longleaf.config" } +}