Improved samplesheet generation for NovaSeqX. #794
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Commented out code deleted. Attributes and methods are ordered more logically. Some private accesors are converted to public. Documentation improved. Added index_read_length and read_length attributes so that these values can be set by the caller.
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jmtcsngr
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Dec 18, 2023
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| C<dragen_max_number_of_configs> - | ||
| DRAGEN analysis can deal with a limited number of distinct | ||
| configurations. Set this attribute if processing off-board. |
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I think file_name may be missing from the documentation?
| - Must be same number of fields (delimited by semicolon) as sequencing and | ||
| indexing reads specified in RunInfo.xml or Reads section. | ||
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| - Indexing reads are specified with I, sequencing reads are specified with |
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Suggested change
| - Indexing reads are specified with I, sequencing reads are specified with | |
| - Indexing reads are specified with 'I', sequencing reads are specified with |
| indexing reads specified in RunInfo.xml or Reads section. | ||
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| - Indexing reads are specified with I, sequencing reads are specified with | ||
| Y, UMI cycles are specified with U, and trimmed reads are specified with N. |
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Suggested change
| Y, UMI cycles are specified with U, and trimmed reads are specified with N. | |
| 'Y', UMI cycles are specified with 'U', and trimmed reads are specified with 'N'. |
| requirements: | ||
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| - Must be same number of fields (delimited by semicolon) as sequencing and | ||
| indexing reads specified in RunInfo.xml or Reads section. |
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Suggested change
| indexing reads specified in RunInfo.xml or Reads section. | |
| indexing reads specified in RunInfo.xml or 'Reads' section. |
| - The number of cycles specified for each read must equal the number of cycles | ||
| specified for that read in the RunInfo.xml file. | ||
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| - Only one Y or I sequence can be specified per read. |
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| - Only one Y or I sequence can be specified per read. | |
| - Only one 'Y' or 'I' sequence can be specified per read. |
| 'lazy_build' => 1, | ||
| 'required' => 0, | ||
| 'documentation' => 'An array containing the length of the first and the ' . | ||
| 'second (if applicable) indexing read..', |
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| 'second (if applicable) indexing read..', | |
| 'second (if applicable) indexing read.', |
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| =cut | ||
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| has 'index_read_length' => ( |
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Is this meant to be used as an override? Should we care if only one is provided at executing time but there are two lengths in LIMS?
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This is when we want to do something semi-manually. Prior to the start of the run we only have LIMS information. If we want to run DRAGEN off-board, then we will find out what happenned from RunInfo.xml As we know only two well, all sorts of discrepancies are possible.
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Commented out code deleted.
Attributes and methods are ordered more logically. Some private accesors are converted to public.
Documentation improved.
Added index_read_length and read_length attributes so that these values can be set by the caller.