From: Ward Vandewege <ward@curii.com>
Date: Wed, 24 Nov 2021 14:47:18 +0000 (-0500)
Subject: 18178: Final tweaks to the debugging blog post CWL.
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/ec904dcdfc5ace2774af00636890f2e6f403839b

18178: Final tweaks to the debugging blog post CWL.

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>
---

diff --git a/blog-examples/debugging/fastq_example/fastqc_blog.yml b/blog-examples/debugging/fastq_example/fastqc_blog.yml
deleted file mode 100644
index dc51512..0000000
--- a/blog-examples/debugging/fastq_example/fastqc_blog.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-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
deleted file mode 100644
index 8171be3..0000000
--- a/blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-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_mismatch.yml b/blog-examples/debugging/fastq_example/fastqc_blog_mismatch.yml
deleted file mode 100644
index d7fd9e0..0000000
--- a/blog-examples/debugging/fastq_example/fastqc_blog_mismatch.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-fastq1:
-  class: Directory 
-  location: keep:c96565a96cd428fe92bf70e97488bd80+21857
-
-fastq2:
-  class: File
-  location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
-
diff --git a/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl b/blog-examples/debugging/fastqc_example/fastqc_blog.cwl
similarity index 99%
rename from blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl
rename to blog-examples/debugging/fastqc_example/fastqc_blog.cwl
index 84b9c40..340c1ec 100644
--- a/blog-examples/debugging/fastq_example/fastqc_blog_fixed.cwl
+++ b/blog-examples/debugging/fastqc_example/fastqc_blog.cwl
@@ -21,7 +21,7 @@ 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)
diff --git a/blog-examples/debugging/fastqc_example/fastqc_blog.yml b/blog-examples/debugging/fastqc_example/fastqc_blog.yml
new file mode 100644
index 0000000..0c56a57
--- /dev/null
+++ b/blog-examples/debugging/fastqc_example/fastqc_blog.yml
@@ -0,0 +1,7 @@
+fastq1:
+  class: File
+  location: keep:be73607762d9948f8da2c1151dc3ef46+70694/ERR2122553_1.fastq.gz
+
+fastq2:
+  class: File
+  location: keep:be73607762d9948f8da2c1151dc3ef46+70694/ERR2122553_2.fastq.gz
diff --git a/blog-examples/debugging/fastq_example/fastqc_blog.cwl b/blog-examples/debugging/fastqc_example/fastqc_blog_broken.cwl
similarity index 84%
rename from blog-examples/debugging/fastq_example/fastqc_blog.cwl
rename to blog-examples/debugging/fastqc_example/fastqc_blog_broken.cwl
index 0949e4a..8d3d348 100644
--- a/blog-examples/debugging/fastq_example/fastqc_blog.cwl
+++ b/blog-examples/debugging/fastqc_example/fastqc_blog_broken.cwl
@@ -5,6 +5,10 @@ label: Quality check on FASTQ
 requirements:
   DockerRequirement:
     dockerPull: biocontainers/fastqc:v0.11.9_cv6
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.fastq1)
+      - $(inputs.fastq2)
 
 hints:
   SoftwareRequirement:
@@ -15,8 +19,9 @@ hints:
 
 inputs:
   fastq1:
-    type: File
+    type: Files
     label: One of set of pair-end FASTQs (R1)
+
   fastq2:
     type: File
     label: One of set of pair-end FASTQs (R2)
@@ -37,8 +42,8 @@ baseCommand: fastqc
 
 arguments:
   - "--noextract"
-  - $(inputs.fastq1.path)
-  - $(inputs.fastq2.path)
+  - $(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
diff --git a/blog-examples/debugging/fastqc_example/fastqc_blog_mismatch.yml b/blog-examples/debugging/fastqc_example/fastqc_blog_mismatch.yml
new file mode 100644
index 0000000..6441654
--- /dev/null
+++ b/blog-examples/debugging/fastqc_example/fastqc_blog_mismatch.yml
@@ -0,0 +1,7 @@
+fastq1:
+  class: Directory
+  location: keep:be73607762d9948f8da2c1151dc3ef46+70694
+
+fastq2:
+  class: File
+  location: keep:be73607762d9948f8da2c1151dc3ef46+70694/ERR2122553_2.fastq.gz