-
Notifications
You must be signed in to change notification settings - Fork 0
/
wf_gcmsearch.cwl
executable file
·52 lines (45 loc) · 1.01 KB
/
wf_gcmsearch.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
#!/usr/bin/env cwl-runner
label: "Run genomic CMsearch (5S rRNA)"
cwlVersion: v1.0
class: Workflow
#requirements:
inputs:
asn_cache: Directory
seqids: File
model_path: File
rfam_amendments: File
rfam_stockholm: File
outputs:
# asncache:
# type: Directory
# outputSource: gpx_qsubmit/asncache
annots:
type: File
outputSource: annot_merge/annots
steps:
gpx_qsubmit:
run: gpx_qsubmit_gcmsearch.cwl
in:
asn_cache: asn_cache
seqids: seqids
out: [asncache, jobs]
cmsearch_wnode:
run: cmsearch_wnode.cwl
in:
asn_cache: gpx_qsubmit/asncache
input_jobs: gpx_qsubmit/jobs
model_path: model_path
rfam_amendments: rfam_amendments
rfam_stockholm: rfam_stockholm
out: [ asncache, outdir ]
gpx_qdump:
run: gpx_qdump.cwl
in:
input_path: cmsearch_wnode/outdir
out: [ annots ]
annot_merge:
run: annot_merge.cwl
in:
asn_cache: cmsearch_wnode/asncache
input: gpx_qdump/annots
out: [ annots ]