datirium · michael-kotliar · Oct 25, 2022 · Nov 7, 2022 · Nov 7, 2022 · Nov 14, 2022
diff --git a/tools/cellbrowser-build-altanalyze.cwl b/tools/cellbrowser-build-altanalyze.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 requirements:

diff --git a/tools/cellbrowser-build-cellranger-arc.cwl b/tools/cellbrowser-build-cellranger-arc.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 requirements:

diff --git a/tools/cellbrowser-build-cellranger-atac.cwl b/tools/cellbrowser-build-cellranger-atac.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 requirements:

diff --git a/tools/cellbrowser-build-cellranger.cwl b/tools/cellbrowser-build-cellranger.cwl
@@ -4,7 +4,7 @@ class: CommandLineTool
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 requirements:

diff --git a/tools/cellranger-arc-aggr.cwl b/tools/cellranger-arc-aggr.cwl
@@ -34,7 +34,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: cumulusprod/cellranger-arc:2.0.2
+  dockerPull: biowardrobe2/cellranger-arc:v0.0.1
 
 
 inputs:

diff --git a/tools/cellranger-arc-count.cwl b/tools/cellranger-arc-count.cwl
@@ -73,7 +73,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: cumulusprod/cellranger-arc:2.0.2
+  dockerPull: biowardrobe2/cellranger-arc:v0.0.1
 
 
 inputs:

diff --git a/tools/cellranger-arc-mkref.cwl b/tools/cellranger-arc-mkref.cwl
@@ -36,7 +36,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: cumulusprod/cellranger-arc:2.0.2
+  dockerPull: biowardrobe2/cellranger-arc:v0.0.1
 
 
 inputs:

diff --git a/tools/deseq-multi-factor.cwl b/tools/deseq-multi-factor.cwl
@@ -8,7 +8,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/deseq:v0.0.6
+  dockerPull: biowardrobe2/deseq:v0.0.7
 
 
 inputs:

diff --git a/tools/fastq-dump.cwl b/tools/fastq-dump.cwl
@@ -168,10 +168,10 @@ outputs:
           return (!!splitted_line.length)?splitted_line:null;
         }
 
-  stdout_log:
+  log_stdout:
     type: stdout
 
-  stderr_log:
+  log_stderr:
     type: stderr
 
 

diff --git a/tools/sc-atac-cluster.cwl b/tools/sc-atac-cluster.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 inputs:
@@ -230,6 +230,14 @@ inputs:
     doc: |
       Export results to UCSC Cell Browser. Default: false
 
+  export_html_report:
+    type: boolean?
+    default: false
+    doc: |
+      Export tehcnical report. HTML format.
+      Note, stdout will be less informative.
+      Default: false
+
   output_prefix:
     type: string?
     inputBinding:
@@ -506,14 +514,25 @@ outputs:
       Seurat object.
       H5AD format.
 
+  sc_report_html_file:
+    type: File?
+    outputBinding:
+      glob: "sc_report.html"
+    doc: |
+      Tehcnical report.
+      HTML format.
+
   stdout_log:
     type: stdout
 
   stderr_log:
     type: stderr
 
 
-baseCommand: ["sc_atac_cluster.R"]
+baseCommand: ["Rscript"]
+arguments:
+- valueFrom: $(inputs.export_html_report?["/usr/local/bin/sc_report_wrapper.R", "/usr/local/bin/sc_atac_cluster.R"]:"/usr/local/bin/sc_atac_cluster.R")
+
 
 stdout: sc_atac_cluster_stdout.log
 stderr: sc_atac_cluster_stderr.log

diff --git a/tools/sc-atac-coverage.cwl b/tools/sc-atac-coverage.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 inputs:
@@ -88,6 +88,14 @@ inputs:
       Print debug information.
       Default: false
 
+  export_html_report:
+    type: boolean?
+    default: false
+    doc: |
+      Export tehcnical report. HTML format.
+      Note, stdout will be less informative.
+      Default: false
+
   output_prefix:
     type: string?
     inputBinding:
@@ -161,14 +169,25 @@ outputs:
       Genome coverage calculated for ATAC fragments
       in bigWig format.
 
+  sc_report_html_file:
+    type: File?
+    outputBinding:
+      glob: "sc_report.html"
+    doc: |
+      Tehcnical report.
+      HTML format.
+
   stdout_log:
     type: stdout
 
   stderr_log:
     type: stderr
 
 
-baseCommand: ["sc_atac_coverage.R"]
+baseCommand: ["Rscript"]
+arguments:
+- valueFrom: $(inputs.export_html_report?["/usr/local/bin/sc_report_wrapper.R", "/usr/local/bin/sc_atac_coverage.R"]:"/usr/local/bin/sc_atac_coverage.R")
+
 
 stdout: sc_atac_coverage_stdout.log
 stderr: sc_atac_coverage_stderr.log

diff --git a/tools/sc-atac-dbinding.cwl b/tools/sc-atac-dbinding.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 inputs:
@@ -259,6 +259,14 @@ inputs:
       Print debug information.
       Default: false
 
+  export_html_report:
+    type: boolean?
+    default: false
+    doc: |
+      Export tehcnical report. HTML format.
+      Note, stdout will be less informative.
+      Default: false
+
   output_prefix:
     type: string?
     inputBinding:
@@ -535,14 +543,25 @@ outputs:
       in the group of cells defined by the
       --second and --groupby parameters.
 
+  sc_report_html_file:
+    type: File?
+    outputBinding:
+      glob: "sc_report.html"
+    doc: |
+      Tehcnical report.
+      HTML format.
+
   stdout_log:
     type: stdout
 
   stderr_log:
     type: stderr
 
 
-baseCommand: ["sc_atac_dbinding.R"]
+baseCommand: ["Rscript"]
+arguments:
+- valueFrom: $(inputs.export_html_report?["/usr/local/bin/sc_report_wrapper.R", "/usr/local/bin/sc_atac_dbinding.R"]:"/usr/local/bin/sc_atac_dbinding.R")
+
 
 stdout: sc_atac_dbinding_stdout.log
 stderr: sc_atac_dbinding_stderr.log

diff --git a/tools/sc-atac-filter.cwl b/tools/sc-atac-filter.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 inputs:
@@ -298,6 +298,14 @@ inputs:
     doc: |
       Export results to UCSC Cell Browser. Default: false
 
+  export_html_report:
+    type: boolean?
+    default: false
+    doc: |
+      Export tehcnical report. HTML format.
+      Note, stdout will be less informative.
+      Default: false
+
   output_prefix:
     type: string?
     inputBinding:
@@ -811,14 +819,25 @@ outputs:
       Seurat object.
       H5AD format
 
+  sc_report_html_file:
+    type: File?
+    outputBinding:
+      glob: "sc_report.html"
+    doc: |
+      Tehcnical report.
+      HTML format.
+
   stdout_log:
     type: stdout
 
   stderr_log:
     type: stderr
 
 
-baseCommand: ["sc_atac_filter.R"]
+baseCommand: ["Rscript"]
+arguments:
+- valueFrom: $(inputs.export_html_report?["/usr/local/bin/sc_report_wrapper.R", "/usr/local/bin/sc_atac_filter.R"]:"/usr/local/bin/sc_atac_filter.R")
+
 
 stdout: sc_atac_filter_stdout.log
 stderr: sc_atac_filter_stderr.log

diff --git a/tools/sc-atac-reduce.cwl b/tools/sc-atac-reduce.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
 - class: DockerRequirement
-  dockerPull: biowardrobe2/sc-tools:v0.0.39
+  dockerPull: biowardrobe2/sc-tools:v0.0.41
 
 
 inputs:
@@ -261,6 +261,14 @@ inputs:
     doc: |
       Export results to UCSC Cell Browser. Default: false
 
+  export_html_report:
+    type: boolean?
+    default: false
+    doc: |
+      Export tehcnical report. HTML format.
+      Note, stdout will be less informative.
+      Default: false
+
   output_prefix:
     type: string?
     inputBinding:
@@ -647,14 +655,25 @@ outputs:
       Seurat object.
       H5AD format.
 
+  sc_report_html_file:
+    type: File?
+    outputBinding:
+      glob: "sc_report.html"
+    doc: |
+      Tehcnical report.
+      HTML format.
+
   stdout_log:
     type: stdout
 
   stderr_log:
     type: stderr
 
 
-baseCommand: ["sc_atac_reduce.R"]
+baseCommand: ["Rscript"]
+arguments:
+- valueFrom: $(inputs.export_html_report?["/usr/local/bin/sc_report_wrapper.R", "/usr/local/bin/sc_atac_reduce.R"]:"/usr/local/bin/sc_atac_reduce.R")
+
 
 stdout: sc_atac_reduce_stdout.log
 stderr: sc_atac_reduce_stderr.log