From 28f4e1a38d8f33aeb4b5348c57ebd2e324c7d431 Mon Sep 17 00:00:00 2001 From: matrulda Date: Wed, 18 Feb 2026 13:18:30 +0100 Subject: [PATCH] Filter out empty fastqs --- main.nf | 16 ++++++++-------- .../AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz | 0 .../AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz | 0 3 files changed, 8 insertions(+), 8 deletions(-) create mode 100644 test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz create mode 100644 test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz diff --git a/main.nf b/main.nf index fd5d72f..9ba5a19 100644 --- a/main.nf +++ b/main.nf @@ -87,15 +87,15 @@ workflow.onComplete { def get_project_and_reads(run_folder) { Channel - .fromPath("${run_folder}/${params.demultiplexer_outdir}/**.fastq.gz" ) - .filter( ~/.*_[^I]\d_001\.fastq\.gz$/ ) - .ifEmpty { "Error: No fastq files found under ${run_folder}/ !\n"; exit 1 } - .map { - it.toString().indexOf('Undetermined') > 0 ? - ['NoProject', it] : - [(it.toString() =~ /^.*\/${params.demultiplexer_outdir}\/([^\/]+)\/.*\.fastq\.gz$/)[0][1],it] + .fromPath("${run_folder}/${params.demultiplexer_outdir}/**.fastq.gz") + .filter { file -> file.name =~ /.*_[^I]\d_001\.fastq\.gz$/ } + .filter { file -> file.size() > 0 } + .ifEmpty { error "Error: No fastq files found under ${run_folder}/!" } + .map { file -> + file.toString().indexOf('Undetermined') > 0 ? + ['NoProject', file] : + [(file.toString() =~ /^.*\/${params.demultiplexer_outdir}\/([^\/]+)\/.*\.fastq\.gz$/)[0][1], file] } - } def combine_results_by_project (fastqc_results,fastq_screen_results,rrna_results) { diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz new file mode 100644 index 0000000..e69de29 diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz new file mode 100644 index 0000000..e69de29