Np fix womtools validation (#1374)

* pin all latest docker version

* loom to h5ad to fix womtools check

* Update ValidateSmartSeq2SingleNucleus.wdl

tests/skylab/smartseq2_single_nucleus/pr/ValidateSmartSeq2SingleNucleus.wdl

@@ -4,20 +4,17 @@ task ValidateSnSmartSeq2 {
     input {
       File exon_intron_counts_hash
       String truth_exon_intron_counts_hash
-      File loom_output
-      File truth_loom
+      File h5ad_output
+      File truth_h5ad
 
-      Int disk_size = ceil(size(loom_output,"GiB") + size(truth_loom, "GiB") + 10)
+      Int disk_size = ceil(size(h5ad_output,"GiB") + size(truth_h5ad, "GiB") + 10)
     }
 
   command <<<
 
     # catch intermittent failures
     set -eo pipefail
 
-    #compare looms
-    python3 /usr/gitc/loomCompare.py --truth-loom ~{truth_loom} --check-loom ~{loom_output} --delta-cutoff 10
-
     # calculate hashes; awk is used to extract the hash from the md5sum output that contains both
     # a hash and the filename that was passed. We parse the first 7 columns because a bug in RSEM
     # makes later columns non-deterministic.
@@ -37,4 +34,4 @@ task ValidateSnSmartSeq2 {
     memory: "8 GB"
     disks: "local-disk 1${disk_size} HDD"
   }
-}
+}

tests/skylab/smartseq2_single_nucleus/pr/test_smartseq2_single_nucleus_PR.wdl

@@ -11,7 +11,7 @@ workflow TestSmartSeq2SingleNucleusPR {
     #checksums
     Array[String] truth_exon_intron_counts_hash
     Array[File] truth_bam
-    File truth_loom
+    File truth_h5ad
 
 
     # snSS2 inputs
@@ -41,8 +41,8 @@ workflow TestSmartSeq2SingleNucleusPR {
       input:
         exon_intron_counts_hash = target_workflow.exon_intron_count_files[idx],
         truth_exon_intron_counts_hash = truth_exon_intron_counts_hash[idx],
-        loom_output = target_workflow.loom_output,
-        truth_loom = truth_loom
+        h5ad_output = target_workflow.h5ad_output,
+        truth_h5ad = truth_h5ad
     }
     call verify_tasks.CompareBams as CompareBams {
       input: