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Changed the MergeBamAlignment task to use --SORT_ORDER "queryname" instead of --SORT_ORDER "unsorted" as this is meant to result in a much more efficient MarkDuplicates task run. Also updated the file names where "unsorted" was used to use "queryname" instead.
to try and get it working from Dockstore/Terra
bshifaw
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Aug 10, 2022
.dockstore.yml
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| - name: processing-for-variant-discovery-gatk4 | ||
| - name: processing-for-variant-discovery-gatk4.wdl | ||
| subclass: WDL | ||
| primaryDescriptorPath: /processing-for-variant-discovery-gatk4 |
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| primaryDescriptorPath: /processing-for-variant-discovery-gatk4 | |
| primaryDescriptorPath: /processing-for-variant-discovery-gatk4.wdl |
bshifaw
reviewed
Aug 10, 2022
.dockstore.yml
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| version: 1.2 | ||
| workflows: | ||
| - name: processing-for-variant-discovery-gatk4 | ||
| - name: processing-for-variant-discovery-gatk4.wdl |
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| - name: processing-for-variant-discovery-gatk4.wdl | |
| - name: processing-for-variant-discovery-gatk4 |
bshifaw
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Looks good to me,
Linking the doc to markduplicates here which indicates that the tool is able to work with query sorted bam file documentation on MarkDuplicates
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Changed the MergeBamAlignment task to use --SORT_ORDER "queryname" instead of --SORT_ORDER "unsorted" as this is meant to result in a much more efficient MarkDuplicates task run.
Also updated the file names where "unsorted" was used to use "queryname" instead.