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-faidx.cwl | 39 ++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 workflows/fastq2fasta/samtools-faidx.cwl

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

diff --git a/workflows/fastq2fasta/samtools-faidx.cwl b/workflows/fastq2fasta/samtools-faidx.cwl
new file mode 100644
index 0000000..5196607
--- /dev/null
+++ b/workflows/fastq2fasta/samtools-faidx.cwl
@@ -0,0 +1,39 @@
+#!/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
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.input_fasta)
+baseCommand: [samtools, faidx]
+inputs:
+  input_fasta:
+    type: File
+    label: "Input fasta"
+    inputBinding:
+      position: 1
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+outputs:
+  indexed_fasta:
+    type: File
+    outputBinding:
+      glob: "$(inputs.input_fasta.basename)"
+    secondaryFiles:
+      - .amb
+      - .ann
+      - .bwt
+      - .pac
+      - .sa
+      - .fai
+  stdout: stdout
+  stderr: stderr
+stdout: samtools-sort-stdout.log
+stderr: samtools-sort-stderr.log
-- 
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