Updating fastq

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog.cwl b/blog-examples/debugging/fastq_example/fastqc_blog.cwl
new file mode 100644 (file)
index 0000000..0949e4a
--- /dev/null
+++ b/blog-examples/debugging/fastq_example/fastqc_blog.cwl
@@ -0,0 +1,48 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Quality check on FASTQ
+
+requirements:
+  DockerRequirement:
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
+
+hints:
+  SoftwareRequirement:
+    packages:
+      FastQC:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
+        version: [ "0.11.9" ]
+
+inputs:
+  fastq1:
+    type: File
+    label: One of set of pair-end FASTQs (R1)
+  fastq2:
+    type: File
+    label: One of set of pair-end FASTQs (R2)
+
+outputs:
+  out-html:
+    type: File[]
+    label: FASTQ QC reports
+    outputBinding:
+      glob: "*html"
+  out-zip:
+    type: File[]
+    label: Zip files of FASTQ QC report and associated data
+    outputBinding:
+      glob: "*fastqc.zip"
+
+baseCommand: fastqc
+
+arguments:
+  - "--noextract"
+  - $(inputs.fastq1.path)
+  - $(inputs.fastq2.path)
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial/blog-examples/debugging
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog.yml b/blog-examples/debugging/fastq_example/fastqc_blog.yml
new file mode 100644 (file)
index 0000000..dc51512
--- /dev/null
+++ b/blog-examples/debugging/fastq_example/fastqc_blog.yml
@@ -0,0 +1,8 @@
+fastq1:
+  class: File
+  location: keep:c96565a96cd428fe92bf70e97488bd80+21857/ERR1726424_1.fastq/ERR1726424_1.fastq.gz
+
+fastq2:
+  class: File
+  location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
+

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl b/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl
new file mode 100644 (file)
index 0000000..8171be3
--- /dev/null
+++ b/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Quality check on FASTQ
+
+requirements:
+  DockerRequirement:
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
+
+inputs:
+  fastq1:
+    type: Files 
+  fastq2:
+    type: File
+
+outputs:
+  out-html:
+    type: File
+    outputBinding:
+      glob: "*html"
+  out-zip:
+    type: File[]
+    outputBinding:
+      glob: "*fastqc.zip"
+
+baseCommand: fastqc
+
+arguments:
+  - $(inputs.fastq1.path)
+  - $(inputs.fastq2.path)

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl b/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl
new file mode 100644 (file)
index 0000000..84b9c40
--- /dev/null
+++ b/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl
@@ -0,0 +1,53 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Quality check on FASTQ
+
+requirements:
+  DockerRequirement:
+    dockerPull: biocontainers/fastqc:v0.11.9_cv6
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.fastq1)
+      - $(inputs.fastq2)
+
+hints:
+  SoftwareRequirement:
+    packages:
+      FastQC:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
+        version: [ "0.11.9" ]
+
+inputs:
+  fastq1:
+    type: File
+    label: One of set of pair-end FASTQs (R1)
+    
+  fastq2:
+    type: File
+    label: One of set of pair-end FASTQs (R2)
+
+outputs:
+  out-html:
+    type: File[]
+    label: FASTQ QC reports
+    outputBinding:
+      glob: "*html"
+  out-zip:
+    type: File[]
+    label: Zip files of FASTQ QC report and associated data
+    outputBinding:
+      glob: "*fastqc.zip"
+
+baseCommand: fastqc
+
+arguments:
+  - "--noextract"
+  - $(inputs.fastq1.basename)
+  - $(inputs.fastq2.basename)
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial/blog-examples/debugging
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog_mismatch.yml b/blog-examples/debugging/fastq_example/fastqc_blog_mismatch.yml
new file mode 100644 (file)
index 0000000..d7fd9e0
--- /dev/null
+++ b/blog-examples/debugging/fastq_example/fastqc_blog_mismatch.yml
@@ -0,0 +1,8 @@
+fastq1:
+  class: Directory 
+  location: keep:c96565a96cd428fe92bf70e97488bd80+21857
+
+fastq2:
+  class: File
+  location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
+