Skip to content

Vg pedigree workflow deepvariant grch38 #837

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

Open
cmarkello wants to merge 8 commits into
base: master
Choose a base branch
from
Open

Vg pedigree workflow deepvariant grch38 #837

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
51a595b
Bumped CADD editor chunking up in the pedigree analysis helper script
cmarkello Aug 19, 2021
e5c44e2
Updated deepvariant container version
cmarkello Aug 20, 2021
f14e54e
Fix setup read helper script for pedigree workflow
cmarkello Aug 21, 2021
836c4f5
Adjusted resource tuning for vg_pedigree workflow. Upgraded to VG 1.34.0
cmarkello Aug 24, 2021
53e156a
Changed abra2 container to a more stable version
cmarkello Aug 27, 2021
87ece7c
Adjusted helper scripts for pedigree workflow to use VG 1.31.0 by def…
cmarkello Aug 27, 2021
778b9bb
remove junk build directory
cmarkello Aug 27, 2021
356ea2d
Merge remote-tracking branch 'upstream/master' into vg_pedigree_workf…
adamnovak Sep 3, 2021
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
2 changes: 1 addition & 1 deletion scripts/vg_pedigree_scripts/setup_input_reads.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ if [ $RUN_SMALL_TEST == false ]; then
INDIVIDUAL_DATA_DIR="${INDIVIDUALS_DATA_DIR}/${SAMPLE_NAME}"
if [ $(find ${INDIVIDUAL_DATA_DIR}/ \( \( \( -wholename '*_R1*.fastq.gz' \) -not -wholename '*WES*' \) -not -wholename '*WTS*' \) | wc -l) -eq 1 ]; then
ln -s $(find ${INDIVIDUAL_DATA_DIR}/ \( \( \( -wholename '*_R1*.fastq.gz' \) -not -wholename '*WES*' \) -not -wholename '*WTS*' \) ) ${READ_DATA_DIR}/${SAMPLE_NAME}_read_pair_1.fq.gz
ln -s $(find ${INDIVIDUAL_DATA_DIR}/ \( \( \( -wholename '*_R1*.fastq.gz' \) -not -wholename '*WES*' \) -not -wholename '*WTS*' \) ) ${READ_DATA_DIR}/${SAMPLE_NAME}_read_pair_2.fq.gz
ln -s $(find ${INDIVIDUAL_DATA_DIR}/ \( \( \( -wholename '*_R2*.fastq.gz' \) -not -wholename '*WES*' \) -not -wholename '*WTS*' \) ) ${READ_DATA_DIR}/${SAMPLE_NAME}_read_pair_2.fq.gz
elif [ $(find ${INDIVIDUAL_DATA_DIR}/ \( \( \( -wholename '*_R1*.fastq.gz' \) -not -wholename '*WES*' \) -not -wholename '*WTS*' \) | wc -l) -gt 1 ]; then
PAIR_1_READS=()
PAIR_2_READS=()
Expand Down
11 changes: 7 additions & 4 deletions scripts/vg_pedigree_scripts/setup_pedigree_script.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -236,6 +236,7 @@ ${RESTART_ARG} \\
--workDir ${COHORT_WORKFLOW_DIR}/tmp \\
--cleanWorkDir onSuccess \\
--whole_genome_config \\
--vg_docker 'quay.io/vgteam/vg:v1.31.0' \\
${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_jobstore \\
${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_outstore \\
${PROBAND_NAME} \\
Expand Down Expand Up @@ -275,8 +276,8 @@ ${SIB_READ_PAIR_LIST} \\
--snpeff_annotation \\
${DRAGEN_ARGS} \\
--run_analysis \\
--cadd_lines 100000 \\
--split_lines 100000 \\
--cadd_lines 30000 \\
--split_lines 30000 \\
--chrom_dir ${CHROM_ANNOT_DIR} \\
--edit_dir ${EDIT_ANNOT_DIR} \\
--cadd_data ${CADD_DATA_DIR} \\
Expand All @@ -293,6 +294,7 @@ ${RESTART_ARG} \\
--logFile ${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_workflow.log \\
--workDir ${COHORT_WORKFLOW_DIR}/tmp \\
--cleanWorkDir always \\
--vg_docker 'quay.io/vgteam/vg:v1.31.0' \\
${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_jobstore \\
${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_outstore \\
${PROBAND_NAME} \\
Expand Down Expand Up @@ -341,6 +343,7 @@ ${RESTART_ARG} \\
--workDir ${COHORT_WORKFLOW_DIR}/tmp \\
--cleanWorkDir onSuccess \\
--whole_genome_config \\
--vg_docker 'quay.io/vgteam/vg:v1.31.0' \\
${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_jobstore \\
${COHORT_WORKFLOW_DIR}/${COHORT_NAME}_pedigree_outstore \\
${PROBAND_NAME} \\
Expand Down Expand Up @@ -379,8 +382,8 @@ ${SIB_READ_PAIR_LIST} \\
--snpeff_annotation \\
${DRAGEN_ARGS} \\
--run_analysis \\
--cadd_lines 100000 \\
--split_lines 100000 \\
--cadd_lines 30000 \\
--split_lines 30000 \\
--chrom_dir ${CHROM_ANNOT_DIR} \\
--edit_dir ${EDIT_ANNOT_DIR} \\
--cadd_data ${CADD_DATA_DIR} \\
Expand Down
6 changes: 3 additions & 3 deletions src/toil_vg/vg_config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -254,7 +254,7 @@
glnexus-docker: 'quay.io/mlin/glnexus:v1.2.7'

# Docker image to use for abra2
abra2-docker: 'dceoy/abra2:latest'
abra2-docker: 'quay.io/biocontainers/abra2:2.24--h7d875b9_0'

# Docker image to use for deeptrio
deeptrio-docker: 'google/deepvariant:deeptrio-1.1.0'
Expand Down Expand Up @@ -394,7 +394,7 @@

# Resources allotted for xg indexing by chromosome (used for GBWT).
gbwt-index-cores: 4
gbwt-index-mem: '50G'
gbwt-index-mem: '10G'
gbwt-index-disk: '100G'
gbwt-index-preemptable: True

Expand Down Expand Up @@ -584,7 +584,7 @@
glnexus-docker: 'quay.io/mlin/glnexus:v1.2.7'

# Docker image to use for abra2
abra2-docker: 'dceoy/abra2:latest'
abra2-docker: 'quay.io/biocontainers/abra2:2.24--h7d875b9_0'

# Docker image to use for deeptrio
deeptrio-docker: 'google/deepvariant:deeptrio-1.1.0'
Expand Down
Loading