Build branch main with version main (b98f636)
Build pipeline: viash-hub.htrnaseq.main-48gzk
Source commit: b98f6367d6
Source message: Add BAM statistics calculations on pool and well level (#6)
This commit is contained in:
@@ -236,7 +236,7 @@ build_info:
|
||||
output: "target/executable/parallel_map"
|
||||
executable: "target/executable/parallel_map/parallel_map"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "21831c2104098ecce57aa9b372e49f865296cc48"
|
||||
git_commit: "b98f6367d672368af134843711a46d3b53717187"
|
||||
git_remote: "https://github.com/viash-hub/htrnaseq"
|
||||
package_config:
|
||||
name: "htrnaseq"
|
||||
|
||||
@@ -516,9 +516,9 @@ RUN wget -O $STAR_TARGET $STAR_SOURCE && \
|
||||
rm $STAR_TARGET && rm -rf /tmp/STAR_$STAR_VERSION
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
|
||||
LABEL org.opencontainers.image.created="2024-08-29T07:58:04Z"
|
||||
LABEL org.opencontainers.image.created="2024-08-29T12:31:01Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
|
||||
LABEL org.opencontainers.image.revision="21831c2104098ecce57aa9b372e49f865296cc48"
|
||||
LABEL org.opencontainers.image.revision="b98f6367d672368af134843711a46d3b53717187"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -0,0 +1,186 @@
|
||||
name: "generate_pool_statistics"
|
||||
namespace: "stats"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--nrReadsNrGenesPerChrom"
|
||||
description: "Path to an output file that contains a .tsv formatted table describing\n\
|
||||
per chromosome the number of reads that were mapped to that chromosome (NumberOfReads\n\
|
||||
column) and the number of genes on that chromosome that had at least one\nread\
|
||||
\ mapped to it (NumberOfGenes).\n"
|
||||
info: null
|
||||
default:
|
||||
- "processedBamFile_well1.tsv"
|
||||
- "processedBamfile_well2.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--nrReadsNrGenesPerChromPool"
|
||||
description: "Pivot table in tsv format of the combined input nrReadsNrGenesPerChrom\
|
||||
\ files. Describes\nper chromosome (as columns) the number of reads, as well\
|
||||
\ as the total number \nof reads per cell barcode and the percentage of nuclear,\
|
||||
\ ERCC and mitochondrial\nreads.\n"
|
||||
info: null
|
||||
example:
|
||||
- "nrReadsNrGenesPerChrom.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/htrnaseq"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "python:3.11-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "pandas"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/stats/generate_pool_statistics/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/stats/generate_pool_statistics"
|
||||
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "b98f6367d672368af134843711a46d3b53717187"
|
||||
git_remote: "https://github.com/viash-hub/htrnaseq"
|
||||
package_config:
|
||||
name: "htrnaseq"
|
||||
version: "main"
|
||||
description: "High-throughput pipeline [WIP]\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC7"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
|
||||
\ dest: 'nextflow_labels.config'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "high-throughput"
|
||||
- "mapping"
|
||||
- "counting"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/htrnaseq"
|
||||
issue_tracker: "https://github.com/viash-hub/htrnaseq/issues"
|
||||
1187
target/executable/stats/generate_pool_statistics/generate_pool_statistics
Executable file
1187
target/executable/stats/generate_pool_statistics/generate_pool_statistics
Executable file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,43 @@
|
||||
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 = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.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)
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,257 @@
|
||||
name: "generate_well_statistics"
|
||||
namespace: "stats"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "The .bam file as returned by the mapping tool STAR."
|
||||
info: null
|
||||
example:
|
||||
- "input.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--barcode"
|
||||
description: "The barcode for the well that is being processed. Is only used to\
|
||||
\ add a metadata\ncolumn to all output files.\n"
|
||||
info: null
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--processedBAMFile"
|
||||
description: "Path to a .tsv file listing, per read in the BAM file,\nthe value\
|
||||
\ for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the\nchromsome\
|
||||
\ to which the read was mapped to.\n"
|
||||
info: null
|
||||
default:
|
||||
- "processedBamFile.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--nrReadsNrGenesPerChrom"
|
||||
description: "Path to an output file that contains a .tsv formatted table describing\n\
|
||||
per chromosome the number of reads that were mapped to that chromosome (NumberOfReads\n\
|
||||
column) and the number of genes on that chromosome that had at least one\nread\
|
||||
\ mapped to it (NumberOfGenes).\n"
|
||||
info: null
|
||||
default:
|
||||
- "nrReadsNrGenesPerChrom.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--nrReadsNrUMIsPerCB"
|
||||
description: "Path to an output file that contains a .tsv formatted table describing\n\
|
||||
per barcode the number of UMI's (nrUMIs) and the total number of reads (NumberOfReads).\n"
|
||||
info: null
|
||||
default:
|
||||
- "nrReadsNrUMIsPerCB.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--umiFreqTop"
|
||||
description: "Path to an output file that contains a .tsv formatted table describing\n\
|
||||
per UMI (column UB) the frequency at which they occur in the reads (column\n\
|
||||
N). Only the top 100 UMIs are included.\n"
|
||||
info: null
|
||||
default:
|
||||
- "umiFreqTop100.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--threads"
|
||||
description: "Number of threads to use for decompressing BAM files.\n"
|
||||
info: null
|
||||
default:
|
||||
- 1
|
||||
required: false
|
||||
min: 1
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Generate summary statistics from BAM files generated by STAR solo."
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test.sam"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/htrnaseq"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
tag: "$id"
|
||||
auto:
|
||||
simplifyInput: true
|
||||
simplifyOutput: false
|
||||
transcript: false
|
||||
publish: false
|
||||
config:
|
||||
labels:
|
||||
mem1gb: "memory = 1000000000.B"
|
||||
mem2gb: "memory = 2000000000.B"
|
||||
mem5gb: "memory = 5000000000.B"
|
||||
mem10gb: "memory = 10000000000.B"
|
||||
mem20gb: "memory = 20000000000.B"
|
||||
mem50gb: "memory = 50000000000.B"
|
||||
mem100gb: "memory = 100000000000.B"
|
||||
mem200gb: "memory = 200000000000.B"
|
||||
mem500gb: "memory = 500000000000.B"
|
||||
mem1tb: "memory = 1000000000000.B"
|
||||
mem2tb: "memory = 2000000000000.B"
|
||||
mem5tb: "memory = 5000000000000.B"
|
||||
mem10tb: "memory = 10000000000000.B"
|
||||
mem20tb: "memory = 20000000000000.B"
|
||||
mem50tb: "memory = 50000000000000.B"
|
||||
mem100tb: "memory = 100000000000000.B"
|
||||
mem200tb: "memory = 200000000000000.B"
|
||||
mem500tb: "memory = 500000000000000.B"
|
||||
mem1gib: "memory = 1073741824.B"
|
||||
mem2gib: "memory = 2147483648.B"
|
||||
mem4gib: "memory = 4294967296.B"
|
||||
mem8gib: "memory = 8589934592.B"
|
||||
mem16gib: "memory = 17179869184.B"
|
||||
mem32gib: "memory = 34359738368.B"
|
||||
mem64gib: "memory = 68719476736.B"
|
||||
mem128gib: "memory = 137438953472.B"
|
||||
mem256gib: "memory = 274877906944.B"
|
||||
mem512gib: "memory = 549755813888.B"
|
||||
mem1tib: "memory = 1099511627776.B"
|
||||
mem2tib: "memory = 2199023255552.B"
|
||||
mem4tib: "memory = 4398046511104.B"
|
||||
mem8tib: "memory = 8796093022208.B"
|
||||
mem16tib: "memory = 17592186044416.B"
|
||||
mem32tib: "memory = 35184372088832.B"
|
||||
mem64tib: "memory = 70368744177664.B"
|
||||
mem128tib: "memory = 140737488355328.B"
|
||||
mem256tib: "memory = 281474976710656.B"
|
||||
mem512tib: "memory = 562949953421312.B"
|
||||
cpu1: "cpus = 1"
|
||||
cpu2: "cpus = 2"
|
||||
cpu5: "cpus = 5"
|
||||
cpu10: "cpus = 10"
|
||||
cpu20: "cpus = 20"
|
||||
cpu50: "cpus = 50"
|
||||
cpu100: "cpus = 100"
|
||||
cpu200: "cpus = 200"
|
||||
cpu500: "cpus = 500"
|
||||
cpu1000: "cpus = 1000"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "debian:stable-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
env:
|
||||
- "PIP_BREAK_SYSTEM_PACKAGES=1"
|
||||
- "HTSLIB_LIBRARY_DIR=/usr/lib/"
|
||||
- "HTSLIB_INCLUDE_DIR=/usr/include/"
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "python3"
|
||||
- "python3-pip"
|
||||
- "python3-venv"
|
||||
- "python-is-python3"
|
||||
- "libhts-dev"
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "pysam"
|
||||
- "pandas"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/stats/generate_well_statistics/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/stats/generate_well_statistics"
|
||||
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "b98f6367d672368af134843711a46d3b53717187"
|
||||
git_remote: "https://github.com/viash-hub/htrnaseq"
|
||||
package_config:
|
||||
name: "htrnaseq"
|
||||
version: "main"
|
||||
description: "High-throughput pipeline [WIP]\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC7"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
|
||||
\ dest: 'nextflow_labels.config'}\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "sequence"
|
||||
- "high-throughput"
|
||||
- "mapping"
|
||||
- "counting"
|
||||
- "pipeline"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/htrnaseq"
|
||||
issue_tracker: "https://github.com/viash-hub/htrnaseq/issues"
|
||||
1319
target/executable/stats/generate_well_statistics/generate_well_statistics
Executable file
1319
target/executable/stats/generate_well_statistics/generate_well_statistics
Executable file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,43 @@
|
||||
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 = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.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)
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user