Changing additional warp-tools docker paths to test h5ad fix

broadinstitute · Nov 20, 2024 · bf65955 · bf65955
1 parent 45a1306
commit bf65955
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
@@ -57,7 +57,7 @@ workflow ATAC {
   String docker_prefix = if cloud_provider == "gcp" then gcr_docker_prefix else acr_docker_prefix
 
   # Docker image names
-  String warp_tools_2_2_0 = "warp-tools:2.2.0"
+  String warp_tools_2_2_0 = "warp-tools:lk-PD-2803-fix-refseq-h5ad"
   String cutadapt_docker = "cutadapt:1.0.0-4.4-1686752919"
   String samtools_docker = "samtools-dist-bwa:3.0.0"
   String upstools_docker = "upstools:1.0.0-2023.03.03-1704300311"

diff --git a/pipelines/skylab/slideseq/SlideSeq.wdl b/pipelines/skylab/slideseq/SlideSeq.wdl
@@ -48,7 +48,7 @@ workflow SlideSeq {
     # docker images
     String pytools_docker = "pytools:1.0.0-1661263730"
     String picard_cloud_docker = "picard-cloud:2.26.10"
-    String warp_tools_docker_2_2_0 = "warp-tools:2.4.0"
+    String warp_tools_docker_2_2_0 = "warp-tools:lk-PD-2803-fix-refseq-h5ad"
     String star_merge_docker = "star-merge-npz:1.3.0"
 
     String ubuntu_docker = "ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf"

diff --git a/tasks/skylab/FastqProcessing.wdl b/tasks/skylab/FastqProcessing.wdl
@@ -138,7 +138,7 @@ task FastqProcessingSlidSeq {
 
 
     # Runtime attributes
-    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:2.3.0"
+    String docker =  "us.gcr.io/broad-gotc-prod/warp-tools:lk-PD-2803-fix-refseq-h5ad"
     Int cpu = 16
     Int machine_mb = 40000
     Int disk = ceil(size(r1_fastq, "GiB")*3 + size(r2_fastq, "GiB")*3) + 50

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
@@ -531,7 +531,7 @@ task SingleNucleusSlideseqH5adOutput {
 task SingleNucleusSmartSeq2H5adOutput {
     input {
         #runtime values
-        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:2.3.0"
+        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:lk-PD-2803-fix-refseq-h5ad"
 
         Array[File] alignment_summary_metrics
         Array[File] dedup_metrics
@@ -626,7 +626,7 @@ task AggregateSmartSeq2H5ad {
         Array[File] h5ad_input
         String batch_id
         String pipeline_version
-        String docker = "us.gcr.io/broad-gotc-prod/warp-tools:2.3.0"
+        String docker = "warp-tools:lk-PD-2803-fix-refseq-h5ad"
         Int disk = 200
         Int machine_mem_mb = 4000
         Int cpu = 1