Open
Conversation
yueyaog
commented
Aug 11, 2023
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/HaplotypeCaller_vcf_gatk4.wdl
Outdated
Show resolved
Hide resolved
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/HaplotypeCaller_vcf_gatk4.wdl
Show resolved
Hide resolved
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/HaplotypeCaller_vcf_gatk4.wdl
Outdated
Show resolved
Hide resolved
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/HaplotypeCaller_vcf_gatk4.wdl
Outdated
Show resolved
Hide resolved
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/HaplotypeCaller_vcf_gatk4.wdl
Show resolved
Hide resolved
GATK_CNV_Mutect2/mutect2-gatk4/m2_subworkflows/calculate_mutational_burden.wdl
Outdated
Show resolved
Hide resolved
| docker: tag_docker | ||
| memory: machine_mem + " MB" | ||
| disks: "local-disk " + select_first([disk_space, 10]) + " HDD" | ||
| preemptible: select_first([preemptible_attempts, 10]) |
Collaborator
Author
There was a problem hiding this comment.
Change the preempt(i/a)ble default to 3 instead of 10
| Boolean? compress_vcfs | ||
| File? gga_vcf | ||
| File? gga_vcf_idx | ||
| String? gcs_project_for_requester_pays |
Collaborator
Author
There was a problem hiding this comment.
Remove this input. We want to localize those input before running GATK tools
MicahR-Y
reviewed
Aug 18, 2023
MicahR-Y
reviewed
Aug 18, 2023
MicahR-Y
reviewed
Aug 18, 2023
yueyaog
commented
Aug 18, 2023
MicahR-Y
reviewed
Dec 7, 2023
| echo "$passing_INDEL" > passing_indel.txt | ||
|
|
||
| #filtered only INDELs | ||
| bcftools isec -C -O v -o ${basename}.indel.filtered.vcf -w1 ${basename}.indel.vcf.gz ${basename}.indel.passing.vcf.gz |
Collaborator
There was a problem hiding this comment.
@yueyaog I think the issue in this task at least is these ${basename} instead of ~{basename}
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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