UMI-tools extract #71
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This reverts commit 38f586b.
rcannood
reviewed
Jul 5, 2024
rcannood
reviewed
Jul 5, 2024
Co-authored-by: Robrecht Cannoodt <[email protected]>
rcannood
reviewed
Jul 5, 2024
rcannood
requested changes
Jul 11, 2024
rcannood
requested changes
Jul 18, 2024
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| - name: --bc_pattern | ||
| type: string | ||
| description: | | ||
| The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides | ||
| of the read are from the UMI. |
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Is this argument not required? Should there not be an alternative -p? What is the difference between -p PATTERN and --bc-pattern and --bc-pattern2?
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I didn't notice that, it only appears in the help message but not in the documentation! I will add it, I believe it is an alternative for --bc-pattern only based on the output i get when using it.
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| - name: --read1_out | ||
| type: file | ||
| required: true | ||
| description: Output file for read 1. | ||
| direction: output | ||
| - name: --read2_out | ||
| type: file | ||
| description: Output file for read 2. | ||
| direction: output |
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Currently:
umi_tools extract:
- Inputs:
- R1:
-I - R2:
--read2-in
- R1:
- Outputs:
- R1:
-S - R2:
--read2-out
- R1:
This component:
- Inputs:
- R1:
--input - R2:
--read2_in
- R1:
- Outputs:
- R1:
--read1_out - R2:
--read2_out
- R1:
I propose changing the inputs of the component to something consistent. Options:
--input,--read2_in,--output,--read2_out--input,--input_r2,--output,--output_r2
Co-authored-by: Robrecht Cannoodt <[email protected]>
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Description
UMI-tools extract
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: