Revise input fields and metadata I/O #50
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- For single-sample input: sample_unique_id, sample_display_name - For multi-sample input: sample_in_metadata Unpack these in the 'laava' named workflow so that single- and multi-sample inputs are equivalent in the downstream processes.
prepare_annotation: Allow nonstandard reference "source type" names
| Terminal Repeat (ITR) regions (see itr_label_1 and itr_label_2 below) or, as a | ||
| legacy mode, one region with the label 'vector', spanning both ITRs (inclusive). | ||
| - May also include additional labeled regions, e.g. for promoter and CDS regions; | ||
| these will be ignored and will not affect the output. |
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We should think about adding a minimal BED file information, in the documentation.
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What additional information would you like to see here? An explanation of the BED format?
workflows/laava/workflow.json
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| "format": "text", | ||
| < 8000 /td> | "hidden": false, | |
| "required": false, | ||
| "default": "ITR", |
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We should keep default to ITR for both first and second ITR.
What is the rational to have first and second, rather than previously left and right?
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From looking at a circular diagram in SnapGene, users might confuse or swap the order of the ITRs in the exported BED/Genbank file. This way, "ITR-R" followed by "ITR-L" will work, even if swapped. As a side effect, entering "ITR" for both itr_label_1 and itr_label_2 works the same as leaving itr_label_2 blank.
First step in revising the classification and output TSV schema for v3.0 -- new input fields.