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

Jump to bottom

Use newer containers for giraffe.wdl #149

Draft
wants to merge 2 commits into
base: master
Choose a base branch
from
Draft

Use newer containers for giraffe.wdl #149

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
27d304f
Depend on bcftools by a tag instead of a removed manifest's hash
adamnovak Jul 5, 2024
f580e24
Split up index reference to depend on different containers
stxue1 Jul 26, 2024
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
80 changes: 65 additions & 15 deletions tasks/bioinfo_utils.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,32 @@
version 1.0

task indexReference {
workflow indexReference {
# This used to be one task, but is split up into two tasks (and one workflow) so we don't need
# to get samtools and picard in one image
input {
File in_reference_file
Int in_index_mem = 4
Int in_index_disk = 2 * round(size(in_reference_file, "G")) + 10
}
call indexReferenceFasta {
input:
in_reference_file = in_reference_file,
in_index_mem = in_index_mem,
in_index_disk = in_index_disk
}
call indexReferenceSequenceDictionary {
input:
in_reference_file = in_reference_file,
in_index_mem = in_index_mem,
in_index_disk = in_index_disk
}
output {
File reference_index_file = indexReferenceFasta.reference_index_file
File reference_dict_file = indexReferenceSequenceDictionary.reference_dict_file
}
}

task indexReferenceFasta {
input {
File in_reference_file
Int in_index_mem = 4
Expand All @@ -12,24 +38,48 @@ task indexReference {

ln -s ~{in_reference_file} ref.fa

# Index the subset reference
samtools faidx ref.fa
# Index the subset reference and save it
samtools faidx ref.fa
>>>

output {
File reference_index_file = "ref.fa.fai"
}

runtime {
preemptible: 2
cpu: 1
memory: in_index_mem + " GB"
disks: "local-disk " + in_index_disk + " SSD"
docker: "biocontainers/samtools:v1.9-4-deb_cv1"
}
}

task indexReferenceSequenceDictionary {
input {
File in_reference_file
Int in_index_mem = 4
Int in_index_disk = 2 * round(size(in_reference_file, "G")) + 10
}
command <<<
set -eux -o pipefail

ln -s ~{in_reference_file} ref.fa

# Save a reference copy by making the dict now
# Make a dict from the reference
java -jar /usr/picard/picard.jar CreateSequenceDictionary \
R=ref.fa \
O=ref.dict
-R ref.fa \
-O ref.dict
>>>
output {
File reference_index_file = "ref.fa.fai"
File reference_dict_file = "ref.dict"
}
runtime {
preemptible: 2
cpu: 1
memory: in_index_mem + " GB"
disks: "local-disk " + in_index_disk + " SSD"
docker: "quay.io/cmarkello/samtools_picard@sha256:e484603c61e1753c349410f0901a7ba43a2e5eb1c6ce9a240b7f737bba661eb4"
docker: "broadinstitute/picard:3.2.0"
}
}

Expand All @@ -52,7 +102,7 @@ task indexVcf {
cpu: 1
memory: in_index_mem + " GB"
disks: "local-disk " + in_index_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand All @@ -78,7 +128,7 @@ task fixVCFContigNaming {
preemptible: 2
memory: in_index_mem + " GB"
disks: "local-disk " + in_index_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand All @@ -101,7 +151,7 @@ task removeHomRefs {
preemptible: 2
memory: in_index_mem + " GB"
disks: "local-disk " + in_index_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down Expand Up @@ -175,7 +225,7 @@ task concatClippedVCFChunks {
memory: mem_gb + " GB"
cpu: 1
disks: "local-disk " + disk_size + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down Expand Up @@ -230,7 +280,7 @@ task sortBAM {
memory: mem_gb + " GB"
cpu: nb_cores
disks: "local-disk " + disk_size + " SSD"
docker: "quay.io/cmarkello/samtools_picard@sha256:e484603c61e1753c349410f0901a7ba43a2e5eb1c6ce9a240b7f737bba661eb4"
docker: "biocontainers/samtools:v1.9-4-deb_cv1"
}
}

Expand Down Expand Up @@ -458,7 +508,7 @@ task splitBAMbyPath {
memory: mem_gb + " GB"
cpu: thread_count
disks: "local-disk " + disk_size + " SSD"
docker: "biocontainers/samtools@sha256:3ff48932a8c38322b0a33635957bc6372727014357b4224d420726da100f5470"
docker: "biocontainers/samtools:v1.9-4-deb_cv1"
}
}

Expand Down Expand Up @@ -499,7 +549,7 @@ task mergeAlignmentBAMChunks {
memory: mem_gb + " GB"
cpu: in_cores
disks: "local-disk " + disk_size + " SSD"
docker: "biocontainers/samtools@sha256:3ff48932a8c38322b0a33635957bc6372727014357b4224d420726da100f5470"
docker: "biocontainers/samtools:v1.9-4-deb_cv1"
}
}

Expand Down
2 changes: 1 addition & 1 deletion workflows/giraffe_and_deeptrio.mapper.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1042,7 +1042,7 @@ task concatClippedVCFChunks {
time: 60
memory: in_call_mem + " GB"
disks: "local-disk " + in_call_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down
2 changes: 1 addition & 1 deletion workflows/giraffe_and_deeptrio.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1291,7 +1291,7 @@ task concatClippedVCFChunks {
time: 60
memory: in_call_mem + " GB"
disks: "local-disk " + in_call_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down
2 changes: 1 addition & 1 deletion workflows/vg_deeptrio_calling_workflow.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -869,7 +869,7 @@ task concatClippedVCFChunks {
time: 60
memory: in_mem + " GB"
disks: "local-disk " + in_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down
6 changes: 3 additions & 3 deletions workflows/vg_multi_map_call.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1429,7 +1429,7 @@ task runVCFClipper {
runtime {
memory: in_vgcall_mem + " GB"
disks: "local-disk " + in_vgcall_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down Expand Up @@ -1465,7 +1465,7 @@ task concatClippedVCFChunks {
time: 60
memory: in_vgcall_mem + " GB"
disks: "local-disk " + in_vgcall_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down Expand Up @@ -1537,7 +1537,7 @@ task normalizeVCF {
cpu: in_vgcall_cores
memory: in_vgcall_mem + " GB"
disks: "local-disk " + in_vgcall_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down
6 changes: 3 additions & 3 deletions workflows/vg_trio_giraffe_deeptrio_workflow.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -531,7 +531,7 @@ task runSplitJointGenotypedVCF {
cpu: in_cores
memory: in_mem + " GB"
disks: "local-disk " + in_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down Expand Up @@ -782,7 +782,7 @@ task concatClippedVCFChunks {
time: 60
memory: in_vgcall_mem + " GB"
disks: "local-disk " + in_vgcall_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down Expand Up @@ -860,7 +860,7 @@ task normalizeVCF {
cpu: in_vgcall_cores
memory: in_vgcall_mem + " GB"
disks: "local-disk " + in_vgcall_disk + " SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down
2 changes: 1 addition & 1 deletion workflows/vg_trio_multi_map_call.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -610,7 +610,7 @@ task runSplitJointGenotypedVCF {
runtime {
memory: 50 + " GB"
disks: "local-disk 100 SSD"
docker: "quay.io/biocontainers/bcftools@sha256:95c212df20552fc74670d8f16d20099d9e76245eda6a1a6cfff4bd39e57be01b"
docker: "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
}
}

Expand Down