millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-21 16:16:04 +00:00
Code Issues Releases Packages Activity

add munin/rnafusion specific config

Browse source
This commit is contained in:
MaxUlysse 2020-03-11 14:02:01 +01:00
parent dd1ddf864b
commit d24a296a01
1 changed files with 64 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

64
conf/pipeline/rnafusion/munin.config Normal file
View file

@ -0,0 +1,64 @@
/*
* -------------------------------------------------
* 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"
}
}