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/samtools-view.cwl | 63 +++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 workflows/fastq2fasta/samtools-view.cwl

(limited to 'workflows/fastq2fasta/samtools-view.cwl')

diff --git a/workflows/fastq2fasta/samtools-view.cwl b/workflows/fastq2fasta/samtools-view.cwl
new file mode 100644
index 0000000..9f11cc6
--- /dev/null
+++ b/workflows/fastq2fasta/samtools-view.cwl
@@ -0,0 +1,63 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "samtools view to convert sam format to bam format"
+requirements:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
+baseCommand: [samtools, view]
+inputs:
+  threads:
+    type: int
+    label: "Number of additional threads to use"
+    default: 4
+    inputBinding:
+      prefix: -@
+  output_bam:
+    type: boolean
+    label: "output BAM"
+    default: true
+    inputBinding:
+      prefix: -b
+  output_filename:
+    type: string
+    label: "output file name"
+    default: "aln.bam"
+    inputBinding:
+      prefix: -o
+  input_file:
+    type: File
+    label: "input file"
+    inputBinding:
+      position: 1
+  include_header:
+    type: boolean
+    label: "include the header in the output"
+    default: false
+    inputBinding:
+      prefix: -h
+  ignore_previous_version:
+    type: boolean
+    label: "ignored for compatibility with previous samtools versions"
+    default: false
+    inputBinding:
+      prefix: -S
+  filter_alignments:
+    type: string?
+    label: "Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]."
+    inputBinding:
+      prefix: -F
+  skip_alignments:
+    type: int?
+    label: "Skip alignments with MAPQ smaller than INT [0]."
+    inputBinding:
+      prefix: -q
+outputs:
+  bam:
+    type: File
+    outputBinding:
+      glob: "$(inputs.output_filename)"
+  stdout: stdout
+  stderr: stderr
+stdout: samtools-view-stdout.log
+stderr: samtools-view-stderr.log
-- 
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