1 files changed, 39 insertions, 0 deletions
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