19 lines
1.5 KiB
Markdown
19 lines
1.5 KiB
Markdown
<!---Example of input directory structure, delete and edit as appropriate per workflow.--->
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This workflow accepts either FASTQ or BAM files as input.
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The FASTQ or BAM input parameters for this workflow accept one of three cases: (i) the path to a single FASTQ or BAM file; (ii) the path to a top-level directory containing FASTQ or BAM files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ or BAM files. In the first and second cases (i and ii), a sample name can be supplied with `--sample`. In the last case (iii), the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`.
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```
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(i) (ii) (iii)
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input_reads.fastq ─── input_directory ─── input_directory
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├── reads0.fastq ├── barcode01
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└── reads1.fastq │ ├── reads0.fastq
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│ └── reads1.fastq
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├── barcode02
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│ ├── reads0.fastq
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│ ├── reads1.fastq
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│ └── reads2.fastq
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└── barcode03
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└── reads0.fastq
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```
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