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mr-c
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May 3, 2023
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I started leaving some comments; most can be applied to other places :-)
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| - doc: "Please provide one sequence file with transcripts. Default: \"\". " | ||
| id: include | ||
| type: | ||
| - "null" | ||
| - string |
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I think this should be a File, yes?
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| - doc: "Please provide one *.genome file created with the genome command. Default: \"\". " | ||
| id: genome | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --genome |
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| - doc: "Directory where input files can be found. Default: \"./\". " | ||
| id: in | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --in |
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This will need overriding. Are there specific file extensions expected?
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| - doc: "Directory, where output files should be saved. Default: \"./\". " | ||
| id: out | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --out |
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This option should be suppressed
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| - doc: "Directory, where output files should be saved. Default: \"./\". " | ||
| id: out | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --out |
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This option should be suppressed
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| - doc: "Sequence file containing minimizers that should not be stored. Default: \"\". " | ||
| id: exclude | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --exclude |
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| - doc: "Define which samples belong together, sum has to be equal to number of sequence files. Default: Every sequence file is one sample from one experiment. Default: []. " | ||
| id: samples | ||
| type: | ||
| - "null" | ||
| - boolean | ||
| inputBinding: | ||
| prefix: --samples |
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| - doc: "If set, names of the experiments are stored in a txt file. Default: 0. " | ||
| id: experiment-names | ||
| type: | ||
| - "null" | ||
| - boolean | ||
| inputBinding: | ||
| prefix: --experiment-names |
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| - doc: "Sequence file containing minimizers, only those minimizers will be considered for determining the expression thresholds. Default: \"\". " | ||
| id: levels-by-genome | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --levels-by-genome |
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| - doc: "Directory, where output files should be saved. Default: \"./\". " | ||
| id: out | ||
| type: | ||
| - "null" | ||
| - string | ||
| inputBinding: | ||
| prefix: --out |
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First try of generated cwl files for needle