diff --git a/README.md b/README.md index ddf9267..50c34aa 100644 --- a/README.md +++ b/README.md @@ -206,6 +206,8 @@ Currently documentation is available for the following pipelines within specific - [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md) - chipseq - [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md) +- demultiplex + - [AWS_TOWER](docs/pipeline/demultiplex/aws_tower.md) - eager - [EVA](docs/pipeline/eager/eva.md) - mag diff --git a/conf/pipeline/demultiplex/aws_tower.config b/conf/pipeline/demultiplex/aws_tower.config new file mode 100644 index 0000000..520487f --- /dev/null +++ b/conf/pipeline/demultiplex/aws_tower.config @@ -0,0 +1,29 @@ +// Profile config names for nf-core/configs + +params { + // Specific nf-core/configs params + config_profile_contact = 'Edmund Miller(@emiller88)' + config_profile_description = 'nf-core/demultiplex AWS Tower profile provided by nf-core/configs' +} + +aws { + batch { + maxParallelTransfers = 24 + maxTransferAttempts = 3 + } + client { + maxConnections = 24 + uploadMaxThreads = 24 + maxErrorRetry = 3 + socketTimeout = 3600000 + uploadRetrySleep = 1000 + uploadChunkSize = 32.MB + } +} + +process { + withName: BASES2FASTQ { + cpus = 16 + memory = 48.GB + } +} diff --git a/docs/pipeline/demultiplex/aws_tower.md b/docs/pipeline/demultiplex/aws_tower.md new file mode 100644 index 0000000..eb87186 --- /dev/null +++ b/docs/pipeline/demultiplex/aws_tower.md @@ -0,0 +1,19 @@ +# nf-core/configs: AWS Tower Demultiplex specific configuration + +Extra specific configuration for demultiplex pipeline + +## Usage + +To use, run the pipeline with `-profile aws_tower`. + +This will download and launch the demultiplex specific [`aws_tower.config`](../../../conf/pipeline/demultiplex/aws_tower.config) which has been pre-configured with a setup suitable for AWS batch through tower. + +Example: `nextflow run nf-core/demultiplex -profile aws_tower` + +## eager specific configurations for eva + +Specific configurations for AWS has been made for demultiplex. + +### General profiles + +- The general AWS Tower profile runs with default nf-core/demultiplex parameters, but with modifications to account file transfer speed and optimized bases2fastq resources. diff --git a/pipeline/demultiplex.config b/pipeline/demultiplex.config new file mode 100644 index 0000000..46c3e08 --- /dev/null +++ b/pipeline/demultiplex.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------- + * nfcore/demultiplex custom profile Nextflow config file + * ------------------------------------------------- + * Config options for custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/demultiplex folder and imported + * under a profile name here. + */ + +profiles { + aws_tower { includeConfig "${params.custom_config_base}/conf/pipeline/demultiplex/aws_tower.config" } +}