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Merge pull request #140 from MaxUlysse/Munin
Update Munin specific configs
This commit is contained in:
Maxime Garcia
GitHub
commit
a3934c84e0
8 changed files with 106 additions and 14 deletions
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@ -167,6 +167,8 @@ Currently documentation is available for the following pipeline within the speci
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* [BINAC](docs/pipeline/ampliseq/binac.md)
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* eager
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* [SHH](docs/pipeline/eager/shh.md)
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* rnafusion
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* [MUNIN](docs/pipeline/rnafusion/munin.md)
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* [UPPMAX](docs/pipeline/sarek/uppmax.md)
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60
conf/pipeline/rnafusion/munin.config
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60
conf/pipeline/rnafusion/munin.config
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@ -0,0 +1,60 @@
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// rnafusion/munin specific profile config
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params {
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max_cpus = 24
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max_memory = 256.GB
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max_time = 72.h
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container_version = '1.1.0'
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// Tool versions
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arriba_version = '1.1.0'
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ericscript_version = '0.5.5'
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fusioncatcher_version = '1.20'
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fusion_inspector_version = '1.3.1-star2.7.0f'
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pizzly_version = '0.37.3'
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squid_version = '1.5-star2.7.0f'
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star_fusion_version = '1.6.0'
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// Paths
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reference_base = '/data1/references/rnafusion'
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containerPath = "file:///data1/containers/rnafusion_containers_v${container_version}"
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containerPathCommon = "file:///data1/containers/rnafusion_common"
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// References
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fasta = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.all.fa"
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gtf = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.gtf"
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transcript = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.cdna.all.fa.gz"
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databases = "${params.reference_base}/1.1.0/databases"
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star_index = "${params.reference_base}/1.1.0/star_index/star"
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arriba_ref = "${params.reference_base}/arriba_ref"
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fusioncatcher_ref = "${params.reference_base}/fusioncatcher_ref/human_v98"
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star_fusion_ref = "${params.reference_base}/star_fusion/1.6.0/ensembl/ctat_genome_lib_build_dir"
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ericscript_ref = "${params.reference_base}/ericscript_ref/ericscript_db_homosapiens_ensembl84"
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}
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process {
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container = "${params.containerPath}/rnafusion_1.1.0.img"
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withName: "arriba|arriba_visualization" {
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container = "${params.containerPath}/rnafusion_arriba_v${params.arriba_version}.img"
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}
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withName: "star_fusion|download_star_fusion" {
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container = "${params.containerPath}/rnafusion_star-fusion_v${params.star_fusion_version}.img"
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}
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withName:fusioncatcher {
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container = "${params.containerPath}/rnafusion_fusioncatcher_v${params.fusioncatcher_version}.img"
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}
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withName:fusion_inspector {
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container = "${params.containerPath}/rnafusion_fusion-inspector_v${params.fusion_inspector_version}.img"
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}
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withName:ericscript {
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container = "${params.containerPathCommon}/rnafusion_ericscript_v${params.ericscript_version}.img"
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}
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withName:pizzly {
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container = "${params.containerPathCommon}/rnafusion_pizzly_v${params.pizzly_version}.img"
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}
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withName:squid {
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container = "${params.containerPath}/rnafusion_squid_v${params.squid_version}.img"
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}
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}
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@ -1,4 +1,4 @@
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// Profile config names for nf-core/configs
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// sarek/munin specific profile config
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params {
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// Specific nf-core/configs params
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@ -6,17 +6,23 @@ params {
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config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs'
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// Specific nf-core/sarek params
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annotation_cache = true
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pon = '/data1/PON/vcfs/BTB.PON.vcf.gz'
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pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi'
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snpEff_cache = '/data1/cache/snpEff/'
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vep_cache = '/data1/cache/VEP/'
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annotation_cache = true
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cadd_cache = true
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cadd_indels = '/data1/cache/CADD/v1.4/InDels.tsv.gz'
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cadd_indels_tbi = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi'
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cadd_wg_snvs = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz'
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cadd_wg_snvs_tbi = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi'
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pon = '/data1/PON/vcfs/BTB.PON.vcf.gz'
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pon_index = '/data1/PON/vcfs/BTB.PON.vcf.gz.tbi'
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snpeff_cache = '/data1/cache/snpEff/'
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vep_cache = '/data1/cache/VEP/'
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vep_cache_version = 95
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}
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// Specific nf-core/sarek process configuration
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process {
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withLabel:sentieon {
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module = {params.sentieon ? 'sentieon/201808.05' : null}
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module = {params.sentieon ? 'sentieon/201911.00' : null}
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container = {params.sentieon ? null : container}
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}
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}
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@ -6,7 +6,7 @@ Extra specific configuration for the ampliseq pipeline.
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To use, run the pipeline with `-profile binac`.
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This will download and launch the ampliseq specific [`binac.config`](../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster.
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This will download and launch the ampliseq specific [`binac.config`](../../../conf/pipeline/ampliseq/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster.
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Example: `nextflow run nf-core/ampliseq -profile binac`
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@ -6,7 +6,7 @@ Extra specific configuration for eager pipeline
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To use, run the pipeline with `-profile shh`.
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This will download and launch the eager specific [`shh.config`](../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster.
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This will download and launch the eager specific [`shh.config`](../../../conf/pipeline/eager/shh.config) which has been pre-configured with a setup suitable for the shh cluster.
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Example: `nextflow run nf-core/eager -profile shh`
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19
docs/pipeline/rnafusion/munin.md
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19
docs/pipeline/rnafusion/munin.md
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@ -0,0 +1,19 @@
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# nf-core/configs: MUNIN rnafusion specific configuration
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Extra specific configuration for rnafusion pipeline
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## Usage
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To use, run the pipeline with `-profile munin`.
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This will download and launch the rnafusion specific [`munin.config`](../../../conf/pipeline/rnafusion/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
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Example: `nextflow run nf-core/rnafusion -profile munin`
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## rnafusion specific configurations for MUNIN
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Specific configurations for `MUNIN` has been made for rnafusion.
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* `cpus`, `memory` and `time` max requirements.
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* Paths to specific containers
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* Paths to specific references and indexes
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@ -6,17 +6,22 @@ Extra specific configuration for sarek pipeline
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To use, run the pipeline with `-profile munin`.
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This will download and launch the sarek specific [`munin.config`](../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
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This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
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Example: `nextflow run nf-core/sarek -profile munin`
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## Sarek specific configurations for MUNIN
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Specific configurations for MUNIN has been made for sarek.
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Specific configurations for `MUNIN` has been made for sarek.
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* Params `annotation_cache` set to `true`
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* Path to `snpEff_cache`: `/data1/cache/snpEff/`
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* Params `annotation_cache` and `cadd_cache` set to `true`
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* Params `vep_cache_version` set to `95`
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* Path to `snpeff_cache`: `/data1/cache/snpEff/`
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* Path to `vep_cache`: `/data1/cache/VEP/`
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* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
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* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
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* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
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* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
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* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
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* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
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* Load module `Sentieon` for Processes with `sentieon` labels
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@ -6,7 +6,7 @@ Extra specific configuration for sarek pipeline
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To use, run the pipeline with `-profile uppmax`.
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This will download and launch the sarek specific [`uppmax.config`](../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
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This will download and launch the sarek specific [`uppmax.config`](../../../conf/pipeline/sarek/uppmax.config) which has been pre-configured with a setup suitable for uppmax clusters.
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Example: `nextflow run nf-core/sarek -profile uppmax`
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