mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-23 00:39:56 +00:00
64 lines
2.4 KiB
Text
64 lines
2.4 KiB
Text
|
/*
|
||
|
|
* -------------------------------------------------
|
||
|
|
* Nextflow config file for Munin Singularity
|
||
|
|
* -------------------------------------------------
|
||
|
|
*/
|
||
|
|
|
||
|
|
params {
|
||
|
|
max_cpus = 24
|
||
|
|
max_memory = 256.GB
|
||
|
|
max_time = 72.h
|
||
|
|
container_version = '1.1.0'
|
||
|
|
|
||
|
|
// Tool versions
|
||
|
|
arriba_version = '1.1.0'
|
||
|
|
ericscript_version = '0.5.5'
|
||
|
|
fusioncatcher_version = '1.20'
|
||
|
|
fusion_inspector_version = '1.3.1-star2.7.0f'
|
||
|
|
pizzly_version = '0.37.3'
|
||
|
|
squid_version = '1.5-star2.7.0f'
|
||
|
|
star_fusion_version = '1.6.0'
|
||
|
|
|
||
|
|
// Paths
|
||
|
|
reference_base = '/data1/references/rnafusion'
|
||
|
|
containerPath = "file:///data1/containers/rnafusion_containers_v${container_version}"
|
||
|
|
containerPathCommon = "file:///data1/containers/rnafusion_common"
|
||
|
|
|
||
|
|
// References
|
||
|
|
fasta = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.all.fa"
|
||
|
|
gtf = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.gtf"
|
||
|
|
transcript = "${params.reference_base}/1.1.0/Homo_sapiens.GRCh38_r97.cdna.all.fa.gz"
|
||
|
|
databases = "${params.reference_base}/1.1.0/databases"
|
||
|
|
|
||
|
|
star_index = "${params.reference_base}/1.1.0/star_index/star"
|
||
|
|
arriba_ref = "${params.reference_base}/arriba_ref"
|
||
|
|
fusioncatcher_ref = "${params.reference_base}/fusioncatcher_ref/human_v98"
|
||
|
|
star_fusion_ref = "${params.reference_base}/star_fusion/1.6.0/ensembl/ctat_genome_lib_build_dir"
|
||
|
|
ericscript_ref = "${params.reference_base}/ericscript_ref/ericscript_db_homosapiens_ensembl84"
|
||
|
|
}
|
||
|
|
|
||
|
|
process {
|
||
|
|
container = "${params.containerPath}/rnafusion_1.1.0.img"
|
||
|
|
|
||
|
|
withName: "arriba|arriba_visualization" {
|
||
|
|
container = "${params.containerPath}/rnafusion_arriba_v${params.arriba_version}.img"
|
||
|
|
}
|
||
|
|
withName: "star_fusion|download_star_fusion" {
|
||
|
|
container = "${params.containerPath}/rnafusion_star-fusion_v${params.star_fusion_version}.img"
|
||
|
|
}
|
||
|
|
withName:fusioncatcher {
|
||
|
|
container = "${params.containerPath}/rnafusion_fusioncatcher_v${params.fusioncatcher_version}.img"
|
||
|
|
}
|
||
|
|
withName:fusion_inspector {
|
||
|
|
container = "${params.containerPath}/rnafusion_fusion-inspector_v${params.fusion_inspector_version}.img"
|
||
|
|
}
|
||
|
|
withName:ericscript {
|
||
|
|
container = "${params.containerPathCommon}/rnafusion_ericscript_v${params.ericscript_version}.img"
|
||
|
|
}
|
||
|
|
withName:pizzly {
|
||
|
|
container = "${params.containerPathCommon}/rnafusion_pizzly_v${params.pizzly_version}.img"
|
||
|
|
}
|
||
|
|
withName:squid {
|
||
|
|
container = "${params.containerPath}/rnafusion_squid_v${params.squid_version}.img"
|
||
|
|
}
|
||
|
|
}
|