From d781e42c9adac07253cb928ae66e9b7314710267 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 12:55:18 -0400
Subject: Move workflows into main repo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 workflows/fastq2fasta/fastq2fasta.cwl | 61 +++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 workflows/fastq2fasta/fastq2fasta.cwl

(limited to 'workflows/fastq2fasta/fastq2fasta.cwl')

diff --git a/workflows/fastq2fasta/fastq2fasta.cwl b/workflows/fastq2fasta/fastq2fasta.cwl
new file mode 100644
index 0000000..0cf5c48
--- /dev/null
+++ b/workflows/fastq2fasta/fastq2fasta.cwl
@@ -0,0 +1,61 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  SubworkflowFeatureRequirement: {}
+hints:
+  ResourceRequirement:
+    ramMin: 3000
+
+inputs:
+  fastq_forward: File
+  fastq_reverse: File?
+  ref_fasta:
+    type: File
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+  threads:
+    type: int
+    default: 4
+  metadata: File?
+
+outputs:
+  out_fasta:
+    type: File
+    outputSource: bam2fasta/out_fasta
+  out_metadata:
+    type: File?
+    outputSource: metadata
+
+steps:
+  bwa-mem:
+    in:
+      threads: threads
+      fastq_forward: fastq_forward
+      fastq_reverse: fastq_reverse
+      index_base: ref_fasta
+    out: [output]
+    run: bwa-mem.cwl
+  samtools-view:
+    in:
+      threads: threads
+      input_file: bwa-mem/output
+    out: [bam]
+    run: samtools-view.cwl
+  samtools-sort:
+    in:
+      input_bamfile: samtools-view/bam
+      threads: threads
+    out: [sorted_bam]
+    run: samtools-sort.cwl
+  bam2fasta:
+    in:
+      bam: samtools-sort/sorted_bam
+      fasta: ref_fasta
+      threads: threads
+    out: [out_fasta]
+    run: bam2fasta.cwl
-- 
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