diff --git a/README.md b/README.md index 398acca..43b8c71 100644 --- a/README.md +++ b/README.md @@ -194,11 +194,13 @@ Currently documentation is available for the following pipelines within specific - [EVA](docs/pipeline/eager/eva.md) - rnafusion - [MUNIN](docs/pipeline/rnafusion/munin.md) +- rnavar + - [MUNIN](docs/pipeline/rnavar/munin.md) - sarek - [MUNIN](docs/pipeline/sarek/munin.md) - [UPPMAX](docs/pipeline/sarek/uppmax.md) -- rnavar - - [MUNIN](docs/pipeline/rnavar/munin.md) +- taxprofiler + - [EVA](docs/pipeline/taxprofiler/eva.md) ### Pipeline-specific documentation diff --git a/conf/pipeline/taxprofiler/eva.config b/conf/pipeline/taxprofiler/eva.config new file mode 100644 index 0000000..59b5fc6 --- /dev/null +++ b/conf/pipeline/taxprofiler/eva.config @@ -0,0 +1,29 @@ +params { + // Specific nf-core/configs params + config_profile_contact = 'James Fellows Yates (@jfy133)' + config_profile_description = 'nf-core/taxprofiler EVA profile provided by nf-core/configs' +} + +process { + + withName: BBMAP_BBDUK { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + } + + withName: MALT_RUN { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + } + + withName: METAPHLAN3 { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + } + + withName: MEGAN_RMA2INFO { + clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + } + +} diff --git a/docs/pipeline/taxprofiler/eva.md b/docs/pipeline/taxprofiler/eva.md new file mode 100644 index 0000000..fc7e3d8 --- /dev/null +++ b/docs/pipeline/taxprofiler/eva.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 eva`. + +This will download and launch the taxprofiler specific [`eva.config`](../../../conf/pipeline/taxprofiler/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster. + +Example: `nextflow run nf-core/taxprofiler -profile eva` + +## taxprofiler specific configurations for eva + +Specific configurations for eva has been made for taxprofiler. + +### General profiles + +- The general MPI-EVA profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues SGE have with Java and python tools, nameling: BBDUK, MALT, MetaPhlAn3, and MEGAN diff --git a/pipeline/taxprofiler.config b/pipeline/taxprofiler.config new file mode 100644 index 0000000..f9eea2d --- /dev/null +++ b/pipeline/taxprofiler.config @@ -0,0 +1,3 @@ +profiles { + eva { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/eva.config" } +}