Merge pull request #22 from yyoshiaki/development1.2.1

vt1.2.1
yyoshiaki · Oct 27, 2020 · 6933b92 · 6933b92
2 parents 32e62a7 + 552916e
commit 6933b92
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# VIRTUS : VIRal Transcript Usage Sensor v1.2 <img src="https://github.com/yyoshiaki/VIRTUS/raw/master/img/VIRTUS.jpg" width="20%" align="right" />
+# VIRTUS : VIRal Transcript Usage Sensor v1.2.1 <img src="https://github.com/yyoshiaki/VIRTUS/raw/master/img/VIRTUS.jpg" width="20%" align="right" />
 
 Virus transcript detection and quantification using normal human RNAseq. VIRTUS is the first tool to detect viral transcripts considering their splicing event rather than the viral genome copy number. VIRTUS can be applied to both bulk RNAseq and single-cell RNAseq. The virus reference covers 762 viruses including SARS-CoV-2 (cause of COVID-19). The workflow is implemented by [Common Workflow Language](https://www.commonwl.org/) and [Rabix](https://rabix.io/). You can specify each parameter individually or give `yaml` or `json` file which describes all the parameter information. In detail, check [the CWL User Guide](http://www.commonwl.org/user_guide/) out. 
 

diff --git a/img/VIRTUS.jpg b/img/VIRTUS.jpg
diff --git a/tool/wget/wget.cwl b/tool/wget/wget.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 doc: The non-interactive network downloader
 requirements:
   DockerRequirement:
-    dockerPull: alpine:3.9
+    dockerPull: inutano/wget:1.20.3-r1
   InlineJavascriptRequirement: {}
 baseCommand: wget
 inputs:

diff --git a/workflow/VIRTUS.PE.cwl b/workflow/VIRTUS.PE.cwl
@@ -3,7 +3,7 @@
 class: Workflow
 cwlVersion: v1.0
 id: VIRTUS.PE
-doc: VIRTUS v1.2
+doc: VIRTUS v1.2.1
 label: VIRTUS.PE
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
@@ -44,6 +44,11 @@ inputs:
     type: int?
     'sbg:x': 805.1641845703125
     'sbg:y': 666.56591796875
+  - id: kz_threshold
+    type: float?
+    doc: 'default : 0.1.'
+    'sbg:x': -296.2785949707031
+    'sbg:y': 411.1441650390625
 outputs:
   - id: Log.out_human
     outputSource:
@@ -312,6 +317,7 @@ steps:
     in:
       - id: threshold
         default: 0.1
+        source: kz_threshold
       - id: input_fq
         source: bedtools_bamtofastq_pe/output_fq2
       - id: output_fq
@@ -326,6 +332,7 @@ steps:
     in:
       - id: threshold
         default: 0.1
+        source: kz_threshold
       - id: input_fq
         source: bedtools_bamtofastq_pe/output_fq1
       - id: output_fq

diff --git a/workflow/VIRTUS.SE.cwl b/workflow/VIRTUS.SE.cwl
@@ -3,7 +3,7 @@
 class: Workflow
 cwlVersion: v1.0
 id: VIRTUS.SE
-doc: VIRTUS v1.2
+doc: VIRTUS v1.2.1
 label: VIRTUS.SE
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
@@ -40,6 +40,11 @@ inputs:
     type: int?
     'sbg:x': 738.9225463867188
     'sbg:y': 519.65234375
+  - id: kz_threshold
+    type: float?
+    doc: 'default : 0.1'
+    'sbg:x': -254.75790405273438
+    'sbg:y': 476.1842956542969
 outputs:
   - id: output_unmapped
     outputSource:
@@ -276,6 +281,7 @@ steps:
     in:
       - id: threshold
         default: 0.1
+        source: kz_threshold
       - id: input_fq
         source: bedtools_bamtofastq_se/output_fq
       - id: output_fq

diff --git a/workflow/createindex.cwl b/workflow/createindex.cwl
@@ -3,8 +3,8 @@
 class: Workflow
 cwlVersion: v1.0
 id: createindex
+doc: VIRTUS v1.2.1
 label: CreateIndex
-doc: VIRTUS v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 inputs:
@@ -94,6 +94,8 @@ steps:
         source: wget_virus/downloaded
       - id: runThreadN
         source: runThreadN
+      - id: genomeSAindexNbases
+        default: 12
     out:
       - id: starIndex
     run: ../tool/star/star_index/star_index.cwl
@@ -133,6 +135,8 @@ steps:
         source: output_name_genomefasta_human
       - id: dir_name
         source: dir_name_STAR_human
+      - id: genomeSAindexNbases
+        default: 14
     out:
       - id: downloaded_genomefasta
       - id: starIndex
@@ -151,8 +155,6 @@ steps:
         default: true
       - id: kmer
         default: 31
-      - id: type
-        default: quasi
     out:
       - id: index
     run: ../tool/salmon-cwl/salmon-index.cwl

diff --git a/workflow/createindex_singlevirus.cwl b/workflow/createindex_singlevirus.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwltool
 
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.2.1
 id: createindex_singlevirus
 label: createindex_singlevirus
 doc: VIRTUS v1.1

diff --git a/workflow/rnaseq-star_index/rnaseq-star_index.cwl b/workflow/rnaseq-star_index/rnaseq-star_index.cwl
@@ -7,8 +7,8 @@ $namespaces:
 inputs:
   - id: runThreadN
     type: int?
-    'sbg:x': -223
-    'sbg:y': -263
+    'sbg:x': -232
+    'sbg:y': -321
   - id: url_genomefasta
     type: string
     'sbg:x': -679
@@ -21,6 +21,10 @@ inputs:
     type: string
     'sbg:x': -505.46875
     'sbg:y': 335
+  - id: genomeSAindexNbases
+    type: int?
+    'sbg:x': -227
+    'sbg:y': -181
 outputs:
   - id: downloaded_genomefasta
     outputSource:
@@ -46,6 +50,7 @@ steps:
         source: runThreadN
       - id: genomeSAindexNbases
         default: 14
+        source: genomeSAindexNbases
     out:
       - id: starIndex
     run: ../../tool/star/star_index/star_index.cwl