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update confs - dev and pride ebi #443

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merged 4 commits into from
Nov 24, 2024
Merged

update confs - dev and pride ebi #443

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27f5200
quantms-utils 0.0.14 -> 0.0.15
ypriverol Nov 24, 2024
b9bb5a9
Merge branch 'dev' of https://github.com/bigbio/quantms into dev
ypriverol Nov 24, 2024
986c179
fixing errors in pride slurm conf
ypriverol Nov 24, 2024
0d79049
fixing errors in pride slurm conf
ypriverol Nov 24, 2024
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2 changes: 1 addition & 1 deletion conf/dev.config
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,6 @@ params {
process {
withLabel: openms {
conda = "bioconda::openms-thirdparty=3.2.0" // The conda package is not the nightly version
container = {"${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'ghcr.io/openms/openms-executables-sif:latest' : 'ghcr.io/openms/openms-executables:latest' }"}
container = {"${ ( workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) && !task.ext.singularity_pull_docker_container ? 'oras://ghcr.io/openms/openms-tools-thirdparty-sif:latest' : 'ghcr.io/openms/openms-tools-thirdparty:latest' }"}
}
}
2 changes: 1 addition & 1 deletion conf/pride_codon_slurm.config
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Expand Up @@ -27,7 +27,7 @@ singularity {
process {
// this is to avoid errors for missing files due to shared filesystem latency
maxRetries = 30
errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" }
errorStrategy = { task.exitStatus in ((130..145) + 104 + 1 + 9 + 134 + 97 + 137 + 0) ? "retry" : "terminate" }
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That looks quite redundant 134 and 137 are between (130..145) 😄 and retry for status 0? Doesn't status 0 mean successful?

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Got it.

cache = "lenient"
afterScript = "sleep 60"

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