made input variables global

gatk-workflows · Dec 20, 2019 · 4e22e97 · 4e22e97
1 parent 3d16e9e
commit 4e22e97
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Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/cram-to-bam.inputs.json b/cram-to-bam.inputs.json
@@ -1,8 +1,8 @@
 {
-  "CramToBamFlow.CramToBamTask.sample_name": "NA12878",
-  "CramToBamFlow.CramToBamTask.input_cram": "gs://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram",
+  "CramToBamFlow.sample_name": "NA12878",
+  "CramToBamFlow.input_cram": "gs://gatk-test-data/wgs_cram/NA12878_20k_hg38/NA12878.cram",
 
-  "CramToBamFlow.CramToBamTask.ref_dict": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict",
-  "CramToBamFlow.CramToBamTask.ref_fasta": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
-  "CramToBamFlow.CramToBamTask.ref_fasta_index": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai"
+  "CramToBamFlow.ref_dict": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict",
+  "CramToBamFlow.ref_fasta": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta",
+  "CramToBamFlow.ref_fasta_index": "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai"
 }
diff --git a/interleaved-fastq-to-paired-fastq.inputs.json b/interleaved-fastq-to-paired-fastq.inputs.json
@@ -1,4 +1,4 @@
 {
-  "UninterleaveFastqs.uninterleave_fqs.input_fastq": "gs://gatk-test-data/wgs_fastq/NA12878_20k/H06JUADXX130110.1.ATCACGAT.20k_interleaved.fastq"
+  "UninterleaveFastqs.input_fastq": "gs://gatk-test-data/wgs_fastq/NA12878_20k/H06JUADXX130110.1.ATCACGAT.20k_interleaved.fastq"
 }
 
diff --git a/interleaved-fastq-to-paired-fastq.wdl b/interleaved-fastq-to-paired-fastq.wdl
@@ -13,8 +13,15 @@ version 1.0
 ##################
 
 workflow UninterleaveFastqs {
+  input {
+    File input_fastq
+  }
 
-  call uninterleave_fqs
+
+  call uninterleave_fqs {
+    input: 
+      input_fastq = input_fastq
+  }
 
 }