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Kp pytools to warptools pd 2186 #1026

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Kp pytools to warptools pd 2186 #1026

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80fc467
Updating feature branch.
kevinpalis Jun 26, 2023
e70e30c
Changing pytools container usage to warp-tools
kevinpalis Jun 26, 2023
665b85f
Changing path to scripts accordingly
kevinpalis Jun 26, 2023
e95ba1b
Changing paths to scripts accordingly
kevinpalis Jun 26, 2023
be4f15c
Updating scatac documentation
kevinpalis Jun 27, 2023
d8898cc
Merge branch 'develop' into kp_pytools_to_warptools_PD-2186
kevinpalis Jun 28, 2023
2bb51c8
Merge branch 'develop' into kp_pytools_to_warptools_PD-2186
kevinpalis Jun 29, 2023
faa9ab4
Merge branch 'develop' into kp_pytools_to_warptools_PD-2186
kevinpalis Jul 5, 2023
ba92e8c
Merge branch 'develop' into kp_pytools_to_warptools_PD-2186
kevinpalis Jul 6, 2023
6c0f3bb
Adding changelog update
kevinpalis Jul 7, 2023
c89b6bf
Updated changelogs and pipeline version numbers.
kevinpalis Jul 7, 2023
1fe0605
Merge branch 'develop' into kp_pytools_to_warptools_PD-2186
kevinpalis Jul 7, 2023
2b4da44
Merge branch 'develop' into kp_pytools_to_warptools_PD-2186
kevinpalis Jul 14, 2023
a3bbe25
Reverting LoomUtils to use pytools again because of some legacy libra…
kevinpalis Jul 14, 2023
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8 changes: 4 additions & 4 deletions beta-pipelines/skylab/ATAC/ATAC.wdl
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Expand Up @@ -241,7 +241,7 @@ task BWAPairedEndAlignment {
read_group_sample_name: "the read group sample to be added upon alignment"
cpu: "the number of cpu cores to use during alignment"
output_base_name: "basename to be used for the output of the task"
docker_image: "the docker image using BWA to be used (default: us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730)"
docker_image: "the docker image using BWA to be used (default: us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671)"
}

# runtime requirements based upon input file size
Expand Down Expand Up @@ -673,13 +673,13 @@ task MakeCompliantBAM {
input {
File bam_input
String output_base_name
String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
}

parameter_meta {
bam_input: "the bam with barcodes in the read ids that need to be converted to barcodes in bam tags"
output_base_name: "base name to be used for the output of the task"
docker_image: "the docker image using the python script to convert the bam barcodes/read ids (default: us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730)"
docker_image: "the docker image using the python script to convert the bam barcodes/read ids (default: us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671)"
}

Int disk_size = ceil(2.5 * (if size(bam_input, "GiB") < 1 then 1 else size(bam_input, "GiB")))
Expand Down Expand Up @@ -707,7 +707,7 @@ task MakeCompliantBAM {
task BreakoutSnap {
input {
File snap_input
String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
String bin_size_list
}
Int num_threads = 1
Expand Down
4 changes: 2 additions & 2 deletions pipelines/skylab/scATAC/scATAC.wdl
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Expand Up @@ -254,7 +254,7 @@ task MakeCompliantBAM {
input {
File input_bam
String output_bam_filename
String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
Int cpu = 1
Int disk = ceil(3 * (size(input_bam, "GiB"))) + 100
Int machine_mem_mb = 4000
Expand Down Expand Up @@ -291,7 +291,7 @@ task MakeCompliantBAM {
task BreakoutSnap {
input {
File snap_input
String docker_image = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker_image = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
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String bin_size_list
String input_id
Int preemptible = 3
Expand Down
6 changes: 3 additions & 3 deletions tasks/skylab/LoomUtils.wdl
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Expand Up @@ -3,7 +3,7 @@ version 1.0
task SmartSeq2LoomOutput {
input {
#runtime values
String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
# the gene count file "<input_id>_rsem.genes.results" in the task results folder call-RSEMExpression
File rsem_gene_results
# file named "<input_id>_QCs.csv" in the folder "call-GroupQCOutputs/glob-*" of the the SS2 output
Expand Down Expand Up @@ -169,7 +169,7 @@ task AggregateSmartSeq2Loom {
String? species
String? organ
String pipeline_version
String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
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Int disk = 200
Int machine_mem_mb = 4000
Int cpu = 1
Expand Down Expand Up @@ -300,7 +300,7 @@ task SingleNucleusOptimusLoomOutput {
task SingleNucleusSmartSeq2LoomOutput {
input {
#runtime values
String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"

Array[File] alignment_summary_metrics
Array[File] dedup_metrics
Expand Down
2 changes: 1 addition & 1 deletion tasks/skylab/StarAlign.wdl
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Expand Up @@ -401,7 +401,7 @@ task MergeStarOutput {
String input_id

#runtime values
String docker = "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
String docker = "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
Int machine_mem_mb = 8250
Int cpu = 1
Int disk = ceil(size(matrix, "Gi") * 2) + 10
Expand Down
2 changes: 1 addition & 1 deletion tests/skylab/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl
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Expand Up @@ -18,7 +18,7 @@ task ValidateSmartSeq2Plate {
>>>

runtime {
docker: "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
docker: "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
cpu: 1
memory: "8 GiB"
disks: "local-disk 1${disk_size} HDD"
Expand Down
2 changes: 1 addition & 1 deletion tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl
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Expand Up @@ -32,7 +32,7 @@ task ValidateSnSmartSeq2 {
>>>

runtime {
docker: "us.gcr.io/broad-gotc-prod/pytools:1.0.0-1661263730"
docker: "us.gcr.io/broad-gotc-prod/warp-tools:1.0.1-1686932671"
cpu: 1
memory: "8 GB"
disks: "local-disk 1${disk_size} HDD"
Expand Down