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Support finding demultiplexing-specific SampleSheet for new MiSeq directory structure #35

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dfornika opened this issue Feb 15, 2024 · 0 comments

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dfornika commented Feb 15, 2024

In the new MiSeq directory structure, there are two SampleSheets:

At the top-level of the run output directory
For a specific Alignment (demultiplexing): Alignment_<N>/<DATE_TIMESTAMP>/SampleSheetUsed.csv

...but we're currently only looking for a SampleSheet named SampleSheet.csv in the top-level of the run dir.

symlink-seqs/symlink-seqs

Lines 462 to 464 in eb38c15

    
           if sequencer_type == 'miseq': 
        
               fastq_subdir = find_miseq_fastq_subdir(run_dir) 
        
               samplesheet_path = os.path.join(run_dir, 'SampleSheet.csv')

We should instead be looking for the SampleSheet for the most recent demultiplexing output dir.

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