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FIX: Strict syntax for proteinfold/nci_gadi #1082

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FIX: Strict syntax for proteinfold/nci_gadi #1082

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eba0527
FIX: Strict syntax for nci_gadi and proteinfold/nci_gadi
maxulysse Apr 7, 2026
dc408f9
restore functionnality
maxulysse Apr 7, 2026
514328f
code polish
maxulysse Apr 7, 2026
ef8f3e5
Merge branch 'master' into conf/nci_gadi.config
maxulysse Apr 14, 2026
c52ed1d
Merge branch 'master' into conf/nci_gadi.config
maxulysse Apr 29, 2026
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9 changes: 2 additions & 7 deletions conf/pipeline/proteinfold/nci_gadi.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,8 @@ profiles {

// Define process resource limits
process {
executor = 'pbspro'
project = System.getenv("PROJECT")
storage = params.storage_account?.trim() ? params.storage_account : "scratch/${params.project}+gdata/${params.project}"
executor = 'pbspro'
module = 'singularity'
cache = 'lenient'
stageInMode = 'symlink'
Expand All @@ -22,7 +21,6 @@ profiles {
withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|RUN_ALPHAFOLD2_MSA' {
queue = params.use_gpu ? 'gpuvolta' : 'normal'
cpus = 48
gpus = 4
time = '4h'
memory = 380.GB
}
Expand All @@ -31,7 +29,6 @@ profiles {
container = "nf-core/proteinfold_colabfold:1.1.1"
queue = params.use_gpu ? 'gpuvolta' : 'normal'
cpus = 48
gpus = 4
time = '4h'
memory = 380.GB
}
Expand All @@ -40,18 +37,16 @@ profiles {
container = "nf-core/proteinfold_esmfold:1.1.1"
queue = params.use_gpu ? 'gpuvolta' : 'normal'
cpus = 48
gpus = 4
time = '4h'
memory = 380.GB
}
}

// Write custom trace file with outputs required for SU calculation
def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
trace {
enabled = true
overwrite = false
file = "./gadi-nf-core-trace-${trace_timestamp}.txt"
file = "./gadi-nf-core-trace-${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.txt"
fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
}
}
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