diff --git a/conf/munin.config b/conf/munin.config index f53def4..e642ec6 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -1,8 +1,13 @@ -//Profile config names for nf-core/configs +// Profile config names for nf-core/configs + params { - config_profile_description = 'MUNIN profile provided by nf-core/configs.' + // Specific nf-core/configs params config_profile_contact = 'Szilveszter Juhos (@szilva)' - config_profile_url = '' + config_profile_description = 'MUNIN profile provided by nf-core/configs.' + config_profile_url = 'https://ki.se/forskning/barntumorbanken' + + // Local AWS iGenomes reference file paths on munin + igenomes_base = '/data1/references/igenomes/' } process { @@ -10,9 +15,10 @@ process { maxForks = 46 } -// To use singularity, use nextflow run -profile munin,singularity +// To use singularity, use nextflow run -profile munin singularity { enabled = true + cacheDir = '/data1/containers/' } // To use docker, use nextflow run -profile munin,docker @@ -20,14 +26,4 @@ docker { enabled = false mountFlags = 'z' fixOwnership = true -} - -params { - // general params - max_memory = 752.GB - max_cpus = 46 - max_time = 72.h - - // Local AWS iGenomes reference file paths on munin - igenomes_base = '/data1/references/igenomes/' -} +} \ No newline at end of file diff --git a/conf/pipeline/sarek/munin.config b/conf/pipeline/sarek/munin.config new file mode 100644 index 0000000..8655a2f --- /dev/null +++ b/conf/pipeline/sarek/munin.config @@ -0,0 +1,26 @@ +// Profile config names for nf-core/configs + +params { + // Specific nf-core/configs params + config_profile_contact = 'Maxime Garcia (@MaxUlysse)' + config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs' + config_profile_url = 'https://ki.se/forskning/barntumorbanken' + + // Specific nf-core/sarek configs params + max_memory = 752.GB + max_cpus = 46 + max_time = 72.h + + // Specific nf-core/sarek params + annotation_cache = true + pon = '/data1/PON/vcfs/BTB.PON.vcf.gz' + pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi' + snpEff_cache = '/data1/cache/snpEff/' + vep_cache = '/data1/cache/VEP/' +} + +// Specific nf-core/sarek configuration +withLabel:sentieon { + module = {params.sentieon ? 'sentieon/201808.05' : ''} + container = {params.sentieon ? '' : 'nfcore/sarek:dev'} +} diff --git a/docs/pipeline/sarek/munin.md b/docs/pipeline/sarek/munin.md new file mode 100644 index 0000000..24c4404 --- /dev/null +++ b/docs/pipeline/sarek/munin.md @@ -0,0 +1,21 @@ +# nf-core/configs: MUNIN sarek specific configuration + +Extra specific configuration for sarek pipeline + +## Usage + +To use, run the pipeline with `-profile munin`. + +This will download and launch the [`munin.config`](../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. + +Example: `nextflow run nf-core/sarek -profile munin` + +## Sarek specific configurations for Munin + +Specific configurations for Munin has been made for sarek. + +* Path to `snpEff_cache`: `/data1/cache/snpEff/` +* Path to `vep_cache`: `/data1/cache/VEP/` +* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz` +* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi` +* Load module `Sentieon` for Process with `sentieon` labels \ No newline at end of file diff --git a/pipeline/sarek.config b/pipeline/sarek.config new file mode 100644 index 0000000..6935794 --- /dev/null +++ b/pipeline/sarek.config @@ -0,0 +1,13 @@ +/* + * ------------------------------------------------- + * nfcore/sarek custom profile Nextflow config file + * ------------------------------------------------- + * Config options for all custom environments. + * Cluster-specific config options should be saved + * in the conf/pipeline/sarek folder and imported + * under a profile name here. + */ + +profiles { + munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" } +} \ No newline at end of file