Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Allow testing Giraffe in small memory #143

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Allow testing Giraffe in small memory #143

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion workflows/giraffe.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -234,7 +234,8 @@ workflow Giraffe {
in_merged_bam_file=mergeAlignmentBAMChunks.merged_bam_file,
in_merged_bam_file_index=mergeAlignmentBAMChunks.merged_bam_file_index,
in_path_list_file=pipeline_path_list_file,
in_prefix_to_strip=REFERENCE_PREFIX
in_prefix_to_strip=REFERENCE_PREFIX,
mem_gb=if MAP_MEM < 20 then MAP_MEM else 20
}

##
Expand Down
3 changes: 2 additions & 1 deletion workflows/giraffe_and_deepvariant.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,8 @@ workflow GiraffeDeepVariant {
in_merged_bam_file=mergeAlignmentBAMChunks.merged_bam_file,
in_merged_bam_file_index=mergeAlignmentBAMChunks.merged_bam_file_index,
in_path_list_file=pipeline_path_list_file,
in_prefix_to_strip=REFERENCE_PREFIX
in_prefix_to_strip=REFERENCE_PREFIX,
mem_gb=if MAP_MEM < 20 then MAP_MEM else 20
}

##
Expand Down
3 changes: 2 additions & 1 deletion workflows/giraffe_and_deepvariant_fromGAF.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,8 @@ workflow GiraffeDeepVariantFromGAF {
in_merged_bam_file=sortBAM.sorted_bam,
in_merged_bam_file_index=sortBAM.sorted_bam_index,
in_path_list_file=pipeline_path_list_file,
in_prefix_to_strip=REFERENCE_PREFIX
in_prefix_to_strip=REFERENCE_PREFIX,
mem_gb=if VG_MEM < 20 then VG_MEM else 20
}

##
Expand Down
3 changes: 2 additions & 1 deletion workflows/vg_indel_realign.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,8 @@ workflow vgMultiMapCall {
in_sample_name=SAMPLE_NAME,
in_merged_bam_file=INPUT_BAM_FILE,
in_merged_bam_file_index=INPUT_BAM_FILE_INDEX,
in_path_list_file=pipeline_path_list_file
in_path_list_file=pipeline_path_list_file,
mem_gb=if MAP_MEM < 20 then MAP_MEM else 20
}
# Run distributed Indel Realignment on contig BAMs
scatter (gatk_caller_input_files in splitBAMbyPath.bams_and_indexes_by_contig) {
Expand Down