M2 cnv updates 1534 #40
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yueyaog
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Aug 11, 2023
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/HaplotypeCaller_vcf_gatk4.wdl
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| docker: tag_docker | ||
| memory: machine_mem + " MB" | ||
| disks: "local-disk " + select_first([disk_space, 10]) + " HDD" | ||
| preemptible: select_first([preemptible_attempts, 10]) |
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Change the preempt(i/a)ble default to 3 instead of 10
| @@ -108,6 +112,7 @@ workflow Mutect2 { | |||
| Boolean? compress_vcfs | |||
| File? gga_vcf | |||
| File? gga_vcf_idx | |||
| String? gcs_project_for_requester_pays | |||
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Remove this input. We want to localize those input before running GATK tools
MicahR-Y
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Aug 18, 2023
MicahR-Y
reviewed
Aug 18, 2023
MicahR-Y
reviewed
Aug 18, 2023
yueyaog
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Aug 18, 2023
MicahR-Y
reviewed
Dec 7, 2023
| echo "$passing_INDEL" > passing_indel.txt | ||
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| #filtered only INDELs | ||
| bcftools isec -C -O v -o ${basename}.indel.filtered.vcf -w1 ${basename}.indel.vcf.gz ${basename}.indel.passing.vcf.gz |
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@yueyaog I think the issue in this task at least is these ${basename} instead of ~{basename}
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I migrated the modifications made by @MicahR-Y in TAG PR 1534 to this PR. I have structured this PR to exclusively present the differences between the official GATK workflows and the TAG workflows.
The incorporation of these changes will lead to the removal of certain approved modifications (those are small changes). Here are the essential changes that should be incorporated: #17 #19 #26