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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/executable/getchromsizes/.config.vsh.yaml
View File

@@ -49,6 +49,9 @@ resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Generates a FASTA file of chromosome sizes and a fasta index file.\n"
test_resources:
- type: "bash_script"
@@ -139,6 +142,8 @@ runners:
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
@@ -167,8 +172,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
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"
@@ -189,8 +194,10 @@ 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'"

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e"
LABEL org.opencontainers.image.created="2024-12-05T08:04:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_MW7eJel8BXirGBmM5nVBbQvzqvrjaH0zDh8H@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="4adb388c7d928eea02bccf890214f3b932b08714"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

44
target/executable/getchromsizes/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)
}
}