aboutsummaryrefslogtreecommitdiff
path: root/workflows/phylogeny/align.cwl
diff options
context:
space:
mode:
authorPjotr Prins2021-01-26 16:22:19 +0000
committerGitHub2021-01-26 16:22:19 +0000
commita54122023ef2bde4ef4fc39355b3491678bbf773 (patch)
tree150bef4a574486db9e7c16d87be89ad219d84bb1 /workflows/phylogeny/align.cwl
parentb112b3203e34ea61dfdf802bce5036f938eaa774 (diff)
parent4842117f530aba08b4a253aee533a8d4802b1c12 (diff)
downloadbh20-seq-resource-a54122023ef2bde4ef4fc39355b3491678bbf773.tar.gz
bh20-seq-resource-a54122023ef2bde4ef4fc39355b3491678bbf773.tar.lz
bh20-seq-resource-a54122023ef2bde4ef4fc39355b3491678bbf773.zip
Merge pull request #124 from urbanslug/master
Add phylogeny workflow
Diffstat (limited to 'workflows/phylogeny/align.cwl')
-rw-r--r--workflows/phylogeny/align.cwl61
1 files changed, 61 insertions, 0 deletions
diff --git a/workflows/phylogeny/align.cwl b/workflows/phylogeny/align.cwl
new file mode 100644
index 0000000..cb2484e
--- /dev/null
+++ b/workflows/phylogeny/align.cwl
@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.1
+
+class: CommandLineTool
+baseCommand: pggb
+
+inputs:
+ threads:
+ type: int
+ inputBinding:
+ position: 1
+ prefix: -t
+
+ pggb_wfmash:
+ type: boolean
+ inputBinding:
+ position: 2
+ prefix: --wfmash
+
+ pggb_fasta:
+ type: File
+ inputBinding:
+ position: 3
+ prefix: -i
+
+ pggb_mash_k_mer:
+ type: int
+ inputBinding:
+ position: 4
+ prefix: -K
+
+ pggb_map_percent_identity:
+ type: int
+ inputBinding:
+ position: 5
+ prefix: -p
+
+ pggb_num_secondary_mappings:
+ type: int
+ inputBinding:
+ position: 6
+ prefix: -n
+
+ pggb_segment_length:
+ type: int
+ inputBinding:
+ position: 7
+ prefix: -s
+
+ pggb_output_dir:
+ type: string
+ inputBinding:
+ position: 8
+ prefix: -o
+
+outputs:
+ pggb_odgi_graph:
+ type: File
+ outputBinding:
+ glob: '*.smooth.og' \ No newline at end of file