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yueyaog
requested changes
Jun 14, 2024
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yueyaog
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Some of the codes are not very robust. Request changes.
| "SomaticRearrangement.Svaba_Annotate_Rscript": "${workspace.svaba_annotations_script}", | ||
| "SomaticRearrangement.annotation_reference_bed": "${workspace.annotation_bed}", | ||
| "SomaticRearrangement.configFile": "${workspace.snpEff_config}", | ||
| "SomaticRearrangement.control_bam": "gs://gptag/tag_183/SM-CEMHS.bam", |
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| command{ | ||
| Rscript ${merge_annotations_script} ${svaba_vcf} ${snpsift_table} \ |
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Submit this R script to Pull Request
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| task snpEffCaller { |
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Do we really need use snpEff here? Is there something more efficient out there?
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Remove this WDL and merge the task to the main SVABA WDL
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| runtime { | ||
| docker: "us.gcr.io/cromptonlab-001-mt/broadinstitute-gatk" | ||
| memory: "2 GB" |
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better to make it flexible
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| task intersectAnnotate { |
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make the commands here less hard-coded
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lots of hard coded things. Better to do it with established tools.
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Adding changes that Mo and I have been working on here: https://github.com/broadinstitute/TAG/issues/1693