millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-25 17:29:55 +00:00
Code Issues Releases Packages Activity

Custom config for nf-core eager on Crick's data and cluster

Browse source
This commit is contained in:
alexandregilardet 2022-03-15 14:13:58 +00:00 committed by GitHub
parent 47bb41a1d8
commit 44696c6040
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 57 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

57
conf/pipeline/eager/custom.config Normal file
View file

@ -0,0 +1,57 @@
/*
* -------------------------------------------------
* Nextflow custom config file for running nf-core eager on data generated at the Francis Crick Institute
* contact: Alexandre Gilardet alexandre.gilardet@crick.ac.uk
* -------------------------------------------------
* nextflow run nf-core/eager -profile <profile>,crick -c custom.config
* (where <profile> is screening or production for low or high-coverage data
* respectively, or external for very high coverage)
*/
profiles {
screening {
process {
withName:bwa {
cpus = 12
memory = '15 GB'
time = '6h'
}
}
}
production {
process {
withName:adapter_removal {
time = '3d'
}
withName:fastp {
time = '8h'
}
withName:bwa {
cpus = 8
memory = '56 GB'
time = '3d'
}
withName:samtools_filter {
time = '3d'
}
withName:dedup {
cpus = 6
memory = '20 GB'
time = '3d'
}
withName:damageprofiler {
memory = '64 GB'
time = '3d'
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
}
}
}
external {
process {
withName:samtools_filter {
cpus = 12
memory = '72 GB'
}
}
}
}