millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-25 01:19:54 +00:00
Code Issues Releases Packages Activity

Modified uppmax and ampliseq specific config to fit with the divided preparation of the database

Browse source
This commit is contained in:
Emelie Nilsso 2020-11-23 21:20:36 +01:00
parent 3cc3445549
commit 2ea06ffab8
1 changed files with 18 additions and 6 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

24
conf/pipeline/ampliseq/uppmax.config
View file

@ -1,15 +1,27 @@
// Profile config names for nf-core/configs
System.err.println("reading from the extra uppmax config, e.g. Daniels")
params {
// Specific nf-core/configs params
config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)'
config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs'
}
withName: make_SILVA_132_16S_classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}
process {
//"make_classifier" is the older version (just one step) of preparing the database for classification
withName: make_classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 -t 7-00:00:00 ${params.clusterOptions ?: ''}" }
}
withName: classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
//"clfr_extract_seq" and "clfr_train" is the newer version, where database preparation is split in two to optimise resources
withName: clfr_extract_seq {
clusterOptions = { "-A $params.project -p core -n 1 -t 7-00:00:00 ${params.clusterOptions ?: ''}" }
}
withName: clfr_train {
clusterOptions = { "-A $params.project -C fat -p node -N 1 -t 24:00:00 ${params.clusterOptions ?: ''}" }
}
withName: classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}
}