Move workflows into main repo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

1 files changed, 59 insertions, 0 deletions

diff --git a/workflows/fastq2fasta/bwa-mem.cwl b/workflows/fastq2fasta/bwa-mem.cwl
new file mode 100644
index 0000000..195411c
--- /dev/null
+++ b/workflows/fastq2fasta/bwa-mem.cwl
@@ -0,0 +1,59 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: CommandLineTool
+doc: string
+requirements:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5
+
+baseCommand: [bwa, mem]
+
+inputs:
+  threads:
+    type: int
+    label: "number of threads"
+    default: 4
+    inputBinding:
+      prefix: -t
+  output_sam:
+    type: string
+    label: "sam file to output results to"
+    default: "out.sam"
+    inputBinding:
+      prefix: -o
+  group_header_line:
+    type: string?
+    label: "read group header line such as '@RG\tID:foo\tSM:bar'"
+    inputBinding:
+      prefix: -R
+  index_base:
+    type: File
+    label: "fasta file for index basename"
+    inputBinding:
+      position: 1
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+  fastq_forward:
+    type: File
+    label: "input fastq file to map (single-end or forward for pair-end)"
+    inputBinding:
+      position: 2
+  fastq_reverse:
+    type: File?
+    label: "input fastq file to map (reverse for pair-end)"
+    inputBinding:
+      position: 3
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: "$(inputs.output_sam)"
+  stdout: stdout
+  stderr: stderr
+stdout: bwa-mem-stdout.log
+stderr: bwa-mem-stderr.log