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ca321ce69d
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last) filters alignments in a MAF file to remove those with too many masked (lower-case) positions compared with their score. As other filter modules like `last/split`, its output file risks to overwrite its input file as their names are constructed from the sample ID when multiple filters are chained in the pipeline. I added a check that gives a clearer error message in this case. Please let me know what you think about; I can add this test to the existing LAST modules as well. This new module is part of the work discribed in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency. We will upgrade it later.
39 lines
1 KiB
YAML
39 lines
1 KiB
YAML
name: last_postmask
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description: Post-alignment masking
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keywords:
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- LAST
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- mask
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- alignment
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- MAF
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tools:
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- last:
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description: LAST finds & aligns related regions of sequences.
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homepage: https://gitlab.com/mcfrith/last
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documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-postmask.rst
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tool_dev_url: https://gitlab.com/mcfrith/last
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doi: "10.1371/journal.pone.0028819"
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licence: ['GPL-3.0-or-later']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- maf:
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type: file
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description: Multiple Aligment Format (MAF) file, compressed with gzip
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pattern: "*.{maf.gz}"
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output:
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- maf:
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type: file
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description: Multiple Aligment Format (MAF) file, compressed with gzip
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pattern: "*.{maf.gz}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@charles-plessy"
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