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Save actual assembler thread count when all available are used #104

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merged 1 commit into from
May 29, 2024
Merged

Save actual assembler thread count when all available are used #104

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8 changes: 6 additions & 2 deletions bin/save_tools_info.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,15 @@ add_version () {
jq -n --arg version "$1" '.version = $version'
}

add_version_and_nproc_value () {
jq -n --arg version "$1" --arg nproc_value "$2" '.version = $version | .nproc_value = $nproc_value'
}

jq -n \
--argjson python "$(add_version "$PYTHON_VERSION")" \
--argjson fastp "$(add_version "$FASTP_VERSION")" \
--argjson unicycler "$(add_version "$UNICYCLER_VERSION")" \
--argjson shovill "$(add_version "$SHOVILL_VERSION")" \
--argjson unicycler "$(add_version_and_nproc_value "$UNICYCLER_VERSION" "$UNICYCLER_NPROC_VALUE")" \
--argjson shovill "$(add_version_and_nproc_value "$SHOVILL_VERSION" "$SHOVILL_NPROC_VALUE")" \
--argjson quast "$(add_version "$QUAST_VERSION")" \
--argjson bwa "$(add_version "$BWA_VERSION")" \
--argjson samtools "$(add_version "$SAMTOOLS_VERSION")" \
Expand Down
23 changes: 18 additions & 5 deletions modules/info.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,8 @@ process TOOLS {
input:
val python_version
val fastp_version
val unicycler_version
val shovill_version
tuple val(unicycler_version), val(unicycler_nproc_value)
tuple val(shovill_version), val(shovill_nproc_value)
val quast_version
val bwa_version
val samtools_version
Expand All @@ -96,7 +96,9 @@ process TOOLS {
PYTHON_VERSION="$python_version"
FASTP_VERSION="$fastp_version"
UNICYCLER_VERSION="$unicycler_version"
UNICYCLER_NPROC_VALUE="$unicycler_nproc_value"
SHOVILL_VERSION="$shovill_version"
SHOVILL_NPROC_VALUE="$shovill_nproc_value"
QUAST_VERSION="$quast_version"
BWA_VERSION="$bwa_version"
SAMTOOLS_VERSION="$samtools_version"
Expand Down Expand Up @@ -153,12 +155,19 @@ process PARSE {
val dbText
val toolText
val imageText
val nprocValue

exec:
def jsonSlurper = new JsonSlurper()

def json = jsonSlurper.parse(new File("${json_file}"))

if (params.assembler == 'unicycler') {
nprocValue = json.unicycler.nproc_value
} else if (params.assembler == 'shovill') {
nprocValue = json.shovill.nproc_value
}

def textRow = { leftSpace, rightSpace, leftContent, rightContent ->
String.format("║ %-${leftSpace}s │ %-${rightSpace}s ║", leftContent, rightContent)
}
Expand Down Expand Up @@ -305,6 +314,7 @@ process PRINT {
val dbText
val toolText
val imageText
val nprocValue

exec:
log.info(
Expand Down Expand Up @@ -332,6 +342,7 @@ process SAVE {
val dbText
val toolText
val imageText
val nprocValue

output:
path "info.txt", emit: info
Expand Down Expand Up @@ -368,7 +379,7 @@ process SAVE {
|${assemblerTextRow('Option', 'Value')}
|╠═══════════════════════════╪═════════════════════════════════════════════════════════════════════╣
|${assemblerTextRow('Assembler', params.assembler.capitalize())}
|${assemblerTextRow('Assembler Thread', params.assembler_thread == 0 ? "0 (All Available)" : params.assembler_thread)}
|${assemblerTextRow('Assembler Thread', params.assembler_thread == 0 ? "${nprocValue} (All Available)" : params.assembler_thread)}
|${assemblerTextRow('Minimum contig length', params.min_contig_length)}
|╚═══════════════════════════╧═════════════════════════════════════════════════════════════════════╝
|""".stripMargin()
Expand Down Expand Up @@ -464,11 +475,12 @@ process UNICYCLER_VERSION {
label 'farm_low'

output:
env VERSION
tuple env(VERSION), env(THREAD)

shell:
$/
VERSION=$(unicycler --version | sed -r "s/.*\sv(.+)/\1/")
THREAD=$(nproc)
/$
}

Expand All @@ -477,11 +489,12 @@ process SHOVILL_VERSION {
label 'farm_low'

output:
env VERSION
tuple env(VERSION), env(THREAD)

shell:
$/
VERSION=$(shovill -v | sed -r "s/.*\s(.+)/\1/")
THREAD=$(nproc)
/$
}

Expand Down