diff --git a/README.md b/README.md index 43b8c71..8acc0d5 100644 --- a/README.md +++ b/README.md @@ -201,6 +201,7 @@ Currently documentation is available for the following pipelines within specific - [UPPMAX](docs/pipeline/sarek/uppmax.md) - taxprofiler - [EVA](docs/pipeline/taxprofiler/eva.md) + - [hasta](docs/pipeline/taxprofiler/hasta.md) ### Pipeline-specific documentation diff --git a/conf/pipeline/taxprofiler/hasta.config b/conf/pipeline/taxprofiler/hasta.config new file mode 100644 index 0000000..1241558 --- /dev/null +++ b/conf/pipeline/taxprofiler/hasta.config @@ -0,0 +1,16 @@ +params { + // Specific nf-core/configs params + config_profile_contact = 'Sofia Stamouli (@sofstam)' + config_profile_description = 'nf-core/taxprofiler HASTA profile provided by nf-core/configs' +} + +process { + + withName:'BBMAP_BBDUK' { + memory = { check_max( 80.GB * task.attempt, 'memory' ) } + } + + withName: 'MALT_RUN' { + memory = { check_max( 80.GB * task.attempt, 'memory' ) } + } +} diff --git a/docs/pipeline/taxprofiler/hasta.md b/docs/pipeline/taxprofiler/hasta.md new file mode 100644 index 0000000..5b49c12 --- /dev/null +++ b/docs/pipeline/taxprofiler/hasta.md @@ -0,0 +1,19 @@ +# nf-core/configs: eva taxprofiler specific configuration + +Extra specific configuration for taxprofiler pipeline + +## Usage + +To use, run the pipeline with `-profile hasta`. + +This will download and launch the taxprofiler specific [`hasta.config`](../../../conf/pipeline/taxprofiler/hasta.config) which has been pre-configured with a setup suitable for the hasta cluster. + +Example: `nextflow run nf-core/taxprofiler -profile hasta` + +## taxprofiler specific configurations for hasta + +Specific configurations for hasta has been made for taxprofiler. + +### General profiles + +- The general hasta profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues with: BBDUK and MALT. diff --git a/pipeline/taxprofiler.config b/pipeline/taxprofiler.config index f9eea2d..0e1dca4 100644 --- a/pipeline/taxprofiler.config +++ b/pipeline/taxprofiler.config @@ -1,3 +1,14 @@ +/* + * ------------------------------------------------- + * nfcore/taxprofiler custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/taxprofiler folder and imported + * under a profile name here. + */ + profiles { + hasta { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/hasta.config" } eva { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/eva.config" } }