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fix issue #5612 - boolean param to optionally log skipped fastqs #5638

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glichtenstein wants to merge 5 commits into from
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fix issue #5612 - boolean param to optionally log skipped fastqs #5638

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22bc6c5
boolean parameter --log_skipped_fastqs added, filename changed to ski…
glichtenstein May 21, 2024
519a943
Final New Line Added
glichtenstein May 21, 2024
7ca0df8
Merge branch 'master' into boolean-parameter-to--log_skipped_fastqs
glichtenstein May 21, 2024
8e87edb
Merge branch 'master' into boolean-parameter-to--log_skipped_fastqs
glichtenstein May 23, 2024
ff2e7d2
log_skipped_fastqs -> log_empty_fastqs
glichtenstein May 24, 2024
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19 changes: 11 additions & 8 deletions subworkflows/nf-core/bcl_demultiplex/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,13 @@ include { BCLCONVERT } from "../../../modules/nf-core/bclconvert/main"
include { BCL2FASTQ } from "../../../modules/nf-core/bcl2fastq/main"

// Define the log file path before the workflow starts
def logFile = new File("${params.outdir}/invalid_fastqs.log")
def logFile = new File("${params.outdir}/skipped_fastqs.log")
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@edmundmiller edmundmiller May 23, 2024

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I think we generally try to avoid using params in subworkflows 😦

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@glichtenstein glichtenstein May 23, 2024

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oh, if not it was ending in some temp workdir, this way it is saved inside the outdir provided in the nextflow run --outdir /some/path/outdir, shall I remove it and leave it as def logFile = new File("skipped_fastqs.log")?


workflow BCL_DEMULTIPLEX {
take:
ch_flowcell // [[id:"", lane:""],samplesheet.csv, path/to/bcl/files]
demultiplexer // bclconvert or bcl2fastq
log_skipped_fastqs // New parameter to control logging of empty FASTQ files

main:
ch_versions = Channel.empty()
Expand Down Expand Up @@ -118,12 +119,14 @@ def generate_fastq_meta(ch_reads, logFile) {
meta.readgroup = readgroup_from_fastq(fastq)
meta.readgroup.SM = meta.samplename
} else {
appendToLogFile(
"Empty or invalid FASTQ file: ${fastq}",
logFile
if (params.log_skipped_fastqs) {
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@edmundmiller edmundmiller May 23, 2024

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Suggested change
if (params.log_skipped_fastqs) {
if (log_skipped_fastqs) {

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@glichtenstein glichtenstein May 23, 2024

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For some reason, when I remove params. I get ERROR ~ No such variable: log_skipped_fastqs

appendToLogFile(
"Empty or invalid FASTQ file: ${fastq}",
logFile
)
fastq = null
}
}
fastq = null
}

return [meta, fastq]
}.filter { it[0] != null }
Expand All @@ -132,8 +135,8 @@ def generate_fastq_meta(ch_reads, logFile) {
// Add meta.single_end
.map { meta, fastq ->
if (meta != null) {
meta.single_end = fastq.size() == 1
}
meta.single_end = fastq.size() == 1
}
return [meta, fastq.flatten()]
}
}
Expand Down