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Bugfix/metadataparser integer overflow #1044

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47aff1b
Update create-aggregate-qc-file.R to handle 32-bit Integer Overflow
gongyixiao Sep 29, 2025
01975cd
Update QcBamAggregate.nf to accept Rscript path from outside of the d…
gongyixiao Sep 29, 2025
8200aa6
Update AggregateFromResult.nf to pass the Rscript path to process
gongyixiao Sep 29, 2025
7bc67e0
Update AggregateFromProcess.nf to pass the Rscript path to process
gongyixiao Sep 29, 2025
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9 changes: 8 additions & 1 deletion containers/metadataparser/create-aggregate-qc-file.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,13 @@
## version = 0.2.1
## status = Dev

install.packages("remotes", repos = "https://cloud.r-project.org", lib = "./")
library(remotes, lib = "./")
remotes::install_version("bit", version = "1.1-12", repos = "https://cloud.r-project.org", lib = "./")
remotes::install_version("bit64", version = "0.9-7", repos = "https://cloud.r-project.org", lib = "./")
library(bit, lib = "./")
library(bit64, lib = "./")

suppressPackageStartupMessages({
library(data.table)
library(parallel)
Expand All @@ -30,7 +37,7 @@ args = parser$parse_args()

## Parse Alfred output ----------------------------------------------------------------------------------------------
read_alfred_qc = function(file) {
input_file = fread(cmd = paste('zgrep ^ME', file, '| cut -f 2-'))
input_file = fread(cmd = paste('zgrep ^ME', file, '| cut -f 2-'), integer64 = "numeric")
## define column TotalReads
input_file[, TotalReads := round(`#Mapped`/MappedFraction)]
##
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5 changes: 3 additions & 2 deletions modules/process/Aggregate/QcBamAggregate.nf
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Expand Up @@ -5,7 +5,8 @@ process QcBamAggregate {

input:
tuple val(cohort), path(alfredIgnoreYTumor), path(alfredIgnoreYNormal), path(alfredIgnoreNTumor), path(alfredIgnoreNNormal), file(hsMetricsTumor), file(hsMetricsNormal)

path(aggregate_qc_Rscript)

output:
path('alignment_qc.txt'), emit: alignmentQcAggregatedOutput

Expand All @@ -17,6 +18,6 @@ process QcBamAggregate {
assayType = 'wgs'
}
"""
Rscript --no-init-file /usr/bin/create-aggregate-qc-file.R -n ${task.cpus} -a ${assayType}
Rscript --no-init-file ${aggregate_qc_Rscript} -n ${task.cpus} -a ${assayType}
"""
}
2 changes: 1 addition & 1 deletion modules/subworkflow/AggregateFromProcess.nf
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Expand Up @@ -279,7 +279,7 @@ workflow aggregateFromProcess
.join(inputHsMetrics)
.set{ inputQcBamAggregate }

QcBamAggregate(inputQcBamAggregate)
QcBamAggregate(inputQcBamAggregate, workflow.projectDir + "/containers/metadataparser/create-aggregate-qc-file.R")
}

if (conpair4Aggregate) {
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2 changes: 1 addition & 1 deletion modules/subworkflow/AggregateFromResult.nf
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Expand Up @@ -136,7 +136,7 @@ workflow aggregateFromResult
inputAlfredIgnoreY.join(inputAlfredIgnoreN)
.join(inputHsMetrics)
.set{ inputQcBamAggregate }
QcBamAggregate(inputQcBamAggregate)
QcBamAggregate(inputQcBamAggregate, workflow.projectDir + "/containers/metadataparser/create-aggregate-qc-file.R")

inputConpairConcord4Aggregate.join(inputConpairContami4Aggregate)
.set{ inputQcConpairAggregate }
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