Move workflows into main repo

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

1 files changed, 41 insertions, 0 deletions

diff --git a/workflows/fastq2fasta/samtools-sort.cwl b/workflows/fastq2fasta/samtools-sort.cwl
new file mode 100644
index 0000000..4c6340c
--- /dev/null
+++ b/workflows/fastq2fasta/samtools-sort.cwl
@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "samtools sort, sort given bam file"
+requirements:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
+baseCommand: [samtools, sort]
+inputs:
+  threads:
+    type: int
+    default: 4
+    inputBinding:
+      prefix: -@
+  tmpfile:
+    type: string
+    default: sort.tmp
+    label: "Write temporary files to PREFIX.nnnn.bam"
+    inputBinding:
+      prefix: -T
+  output_bam:
+    type: string
+    default: aln.sorted.bam
+    label: "Write final output to FILENAME"
+    inputBinding:
+      prefix: -o
+  input_bamfile:
+    type: File
+    label: "Input bamfile"
+    inputBinding:
+      position: 1
+
+outputs:
+  sorted_bam:
+    type: File
+    outputBinding:
+      glob: "$(inputs.output_bam)"
+  stdout: stdout
+  stderr: stderr
+stdout: samtools-sort-stdout.log
+stderr: samtools-sort-stderr.log