Snakemake Picard IlluminaBaseCallsToSam Wrapper Example

demux-wrapper-example.Snakefile

rule illumina_basecalls_to_sam:
    input:
        basecalls_dir=basecalls_dir,
        barcodes_dir=rules.extract_illumina_barcodes.output.barcodes_dir,
        library_params=rules.create_basecalling_params.output.library_params
    output: list_unmerged_sample_bam()
    threads: max(1, int(threads / len(lanes)))
    resources:
        gc_time_limit=50,
        gc_heap_free_limit=10,
        malloc=lambda wildcards, attempt: int(attempt * 1.5 * 8192),
        samjdk_buffer_size=131072,
        use_async_io_read_samtools=1,
        use_async_io_write_samtools=1
    params:
        lane='{lane}',
        create_index=True,
        run_barcode=run_barcode,
        platform=None,
        sequencing_center=sequencing_center,
        run_start_date=run_start_date,
        read_structure=read_structure,
        adapters_to_check=['INDEXED', 'NEXTERA_V2', 'FLUIDIGM'],
        include_non_pf_reads=False
    log: f'{run_output}/logs/IlluminaBasecallsToSam.{{lane}}.log'
    wrapper: f'{wrapper_uri}/picard_illumina_basecalls_to_sam'