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Add FASTQ header cleaning as the first pipeline step - #35
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Some FASTQ files carry spaces in their header lines (for example "@Readid 1:N:0:INDEX"). Tools further down the pipeline truncate read names at the first space, which breaks UMI extraction and read-name matching after alignment. CLEAN_FASTQ_HEADERS replaces every space in a header line with an underscore. It runs on the raw reads immediately after the samplesheet is parsed, before UMI moving, trimming and alignment, and reassigns ch_fastq the same way the surrounding steps do, so nothing downstream needed changing. Sequence and quality lines are passed through untouched. Off by default; enable with --clean_fastq_headers. The cleaned reads are intermediates and are not published. TrimGalore re-links its input to "${prefix}.fastq.gz", so downstream published file names are unchanged. pigz signals a corrupt or truncated input by exiting non-zero after emitting a partial stream, so both ends of the pipe are checked and the record count is validated; otherwise the task would succeed and hand a silently truncated FASTQ to the rest of the pipeline. The pipeline is single-end only - single_end is parsed into meta but never read downstream - so the module accepts exactly one FASTQ per sample and fails loudly on anything else. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Some FASTQ files carry spaces in their header lines (for example "ID 1:N:0:INDEX"). Tools further down the pipeline truncate read names at the first space, which breaks UMI extraction and read-name matching after alignment (samtools).
CLEAN_FASTQ_HEADERS replaces every space in a header line with an underscore. It runs on the raw reads immediately after the samplesheet is parsed, before UMI moving, trimming and alignment, and reassigns ch_fastq the same way the surrounding steps do. Sequence and quality lines are passed through untouched.
Off by default, enable with --clean_fastq_headers.
The cleaned reads are intermediates and are not published. TrimGalore re-links its input to "${prefix}.fastq.gz", so downstream published file names are unchanged. pigz signals a corrupt or truncated input by exiting non-zero after emitting a partial stream, so both ends of the pipe are checked and the record count is validated.