mirror of
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60 lines
2.3 KiB
Text
60 lines
2.3 KiB
Text
// 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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