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Build branch main with version main (4adb388)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-c9pqm

Source commit: 4adb388c7d

Source message: Merge pull request #29 from viash-hub/add-labels

Add labels (and then some)
This commit is contained in:
CI
2024-12-05 08:52:37 +00:00
parent b649544267
commit d69226987e
371 changed files with 11102 additions and 6497 deletions
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15
target/nextflow/stringtie/.config.vsh.yaml
View File

@@ -97,6 +97,9 @@ resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Transcript assembly and quantification for RNA-Seq\n"
test_resources:
- type: "bash_script"
@@ -189,6 +192,8 @@ runners:
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
@@ -216,8 +221,8 @@ build_info:
output: "target/nextflow/stringtie"
executable: "target/nextflow/stringtie/main.nf"
viash_version: "0.9.0"
git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e"
git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
git_commit: "4adb388c7d928eea02bccf890214f3b932b08714"
git_remote: "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
@@ -238,8 +243,10 @@ package_config:
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
\ := '$id'\n"
- ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
\ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
\ := '$id'\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"

16
target/nextflow/stringtie/main.nf
View File

@@ -2923,6 +2923,11 @@ meta = [
"type" : "bash_script",
"path" : "script.sh",
"is_executable" : true
},
{
"type" : "file",
"path" : "/src/workflows/utils/labels.config",
"dest" : "nextflow_labels.config"
}
],
"description" : "Transcript assembly and quantification for RNA-Seq\n",
@@ -3039,7 +3044,10 @@ meta = [
"cpu200" : "cpus = 200",
"cpu500" : "cpus = 500",
"cpu1000" : "cpus = 1000"
}
},
"script" : [
"includeConfig(\\"nextflow_labels.config\\")"
]
},
"debug" : false,
"container" : "docker"
@@ -3073,8 +3081,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/stringtie",
"viash_version" : "0.9.0",
"git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e",
"git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
"git_commit" : "4adb388c7d928eea02bccf890214f3b932b08714",
"git_remote" : "https://x-access-token:ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",
@@ -3105,7 +3113,7 @@ meta = [
"source" : "/workdir/root/repo/src",
"target" : "/workdir/root/repo/target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n",
".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

2
target/nextflow/stringtie/nextflow.config
View File

@@ -122,4 +122,4 @@ process{
withLabel: cpu1000 { cpus = 1000 }
}
includeConfig("nextflow_labels.config")

44
target/nextflow/stringtie/nextflow_labels.config Normal file
View File

@@ -0,0 +1,44 @@
process {
// Default resources for components that hardly do any processing
memory = { 2.GB * task.attempt }
cpus = 1
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = null
// Resource labels
withLabel: singlecpu { cpus = 1 }
withLabel: lowcpu { cpus = 2 }
withLabel: midcpu { cpus = 4 }
withLabel: highcpu { cpus = 8 }
withLabel: veryhighcpu { cpus = 16 }
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
withLabel: veryhighmem { memory = { get_memory( 48.GB * task.attempt ) } }
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}