1 files changed, 41 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl
new file mode 100644
index 0000000..dab7ff2
--- /dev/null
+++ b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl
@@ -0,0 +1,41 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  SubworkflowFeatureRequirement: {}
+hints:
+  ResourceRequirement:
+    ramMin: 3000
+
+inputs:
+  ref_fasta:
+    type: File
+  fastq_forward:
+    type: File
+  fastq_reverse:
+    type: File?
+  threads:
+    type: int
+    default: 4
+
+outputs:
+  out_fasta:
+    type: File
+    outputSource: fastq2fasta/out_fasta
+
+steps:
+  bwa-index:
+    in: {input_fasta: ref_fasta}
+    out: [indexed_fasta]
+    run: bwa-index.cwl
+  samtools-faidx:
+    in: {input_fasta: bwa-index/indexed_fasta}
+    out: [indexed_fasta]
+    run: samtools-faidx.cwl
+  fastq2fasta:
+    in:
+      fastq_forward: fastq_forward
+      fastq_reverse: fastq_reverse
+      ref_fasta: samtools-faidx/indexed_fasta
+      threads: threads
+    out: [out_fasta]
+    run: fastq2fasta.cwl