Add --include-introns and --expect-cells

Author: hisplan

CellRangerGex.deps.zip

@@ -10,6 +10,9 @@ workflow CellRangerGex {
         Array[File] inputFastq
         String referenceUrl
 
+        Boolean includeIntrons
+        Int? expectCells
+
         Int numCores = 16
         Int memory = 128
 
@@ -23,6 +26,8 @@ workflow CellRangerGex {
             fastqName = fastqName,
             inputFastq = inputFastq,
             referenceUrl = referenceUrl,
+            includeIntrons = includeIntrons,
+            expectCells = expectCells,
             numCores = numCores,
             memory = memory,
             dockerRegistry = dockerRegistry

CellRangerGex.wdl

@@ -10,6 +10,8 @@
         "s3://dp-lab-test/tiny/cellranger_tiny_fastq/tinygex_S1_L002_R2_001.fastq.gz"
     ],
     "CellRangerGex.referenceUrl": "https://dp-lab-test.s3.amazonaws.com/tiny/cellranger_tiny_ref/refdata-gex.tar.gz",
+    "CellRangerGex.includeIntrons": true,
+    "CellRangerGex.expectCells": 1000,    
     "CellRangerGex.memory": 128,
     "CellRangerGex.dockerRegistry": "quay.io/hisplan"
 }

configs/devtest.inputs.json

@@ -7,6 +7,8 @@
         "s3://.../test_sample1_S1_L001_R2_001.fastq.gz"
     ],
     "CellRangerGex.referenceUrl": "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz",
+    "CellRangerGex.includeIntrons": false,
+    "CellRangerGex.expectCells": 1000,
     "CellRangerGex.memory": 128,
     "CellRangerGex.dockerRegistry": "quay.io/hisplan"
 }

configs/template.inputs.json

@@ -8,6 +8,9 @@ task Count {
         Array[File] inputFastq
         String referenceUrl
 
+        Boolean includeIntrons
+        Int? expectCells = 3000
+
         Int numCores = 16
         Int memory = 128
 
@@ -47,7 +50,8 @@ task Count {
             --fastqs=${path_input} \
             --sample=~{fastqName} \
             --localcores=~{numCores} \
-            --localmem=~{localMemory}
+            --localmem=~{localMemory} \
+            --expect-cells=~{expectCells} ~{true='--include-introns' false='' includeIntrons}
 
         # targz the analysis folder and pipestance metadata if successful
         if [ $? -eq 0 ]

modules/Count.wdl

@@ -8,6 +8,8 @@
         "s3://dp-lab-data/collaborators/arudensky/Cd4CellDiffAf/Foxp3_minus/FASTQ/2676_Foxp3_minus_IGO_12104_3_S25_L001_R2_001.fastq.gz"
     ],
     "Count.referenceUrl": "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz",
+    "Count.includeIntrons": false,
+    "Count.expectCells": 3000,
     "Count.numCores": 16,
     "Count.memory": 128,
     "Count.dockerRegistry": "quay.io/hisplan"

tests/test.Count.inputs.json

@@ -10,6 +10,9 @@ workflow Count {
         Array[File] inputFastq
         String referenceUrl
 
+        Boolean includeIntrons
+        Int? expectCells
+
         Int numCores
         Int memory
 
@@ -21,10 +24,12 @@ workflow Count {
         input:
             sampleName = sampleName,
             fastqName = fastqName,
-            inputFastq = inputFastq,            
+            inputFastq = inputFastq,
             referenceUrl = referenceUrl,
+            includeIntrons = includeIntrons,
+            expectCells = expectCells,
             numCores = numCores,
-            memory = memory,            
+            memory = memory,
             dockerRegistry = dockerRegistry
     }