diff --git a/README.md b/README.md index 72797f9..c42981e 100644 --- a/README.md +++ b/README.md @@ -193,6 +193,8 @@ Currently documentation is available for the following pipelines within specific - [UPPMAX](docs/pipeline/ampliseq/uppmax.md) - eager - [EVA](docs/pipeline/eager/eva.md) +- mag + - [EVA](docs/pipeline/mag/eva.md) - rnafusion - [MUNIN](docs/pipeline/rnafusion/munin.md) - rnavar diff --git a/conf/pipeline/mag/eva.config b/conf/pipeline/mag/eva.config new file mode 100644 index 0000000..81d8d0c --- /dev/null +++ b/conf/pipeline/mag/eva.config @@ -0,0 +1,14 @@ +params { + // Specific nf-core/configs params + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs' +} + +process { + + withName: FASTQC { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + } + +} diff --git a/docs/pipeline/eager/mpcdf.config b/docs/pipeline/eager/mpcdf.md similarity index 100% rename from docs/pipeline/eager/mpcdf.config rename to docs/pipeline/eager/mpcdf.md diff --git a/docs/pipeline/mag/eva.md b/docs/pipeline/mag/eva.md new file mode 100644 index 0000000..7d98117 --- /dev/null +++ b/docs/pipeline/mag/eva.md @@ -0,0 +1,15 @@ +# nf-core/configs: eva mag specific configuration + +Extra specific configuration for mag pipeline + +## Usage + +To use, run the pipeline with `-profile eva`. + +This will download and launch the mag specific [`eva.config`](../../../conf/pipeline/mag/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster. + +Example: `nextflow run nf-core/mag -profile eva` + +## mag specific configurations for eva + +Specific configurations for eva has been made for mag, primarily adjusting SGE memory requirements of Java tools (e.g. FastQC). diff --git a/pipeline/mag.config b/pipeline/mag.config new file mode 100644 index 0000000..979392f --- /dev/null +++ b/pipeline/mag.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------- + * nfcore/mag custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/mag folder and imported + * under a profile name here. + */ + +profiles { + eva { includeConfig "${params.custom_config_base}/conf/pipeline/mag/eva.config" } +}