Merge branch 'blog-examples'

refs #18178

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

diff --git a/blog-examples/debugging/fastqc/fastqc_blog.cwl b/blog-examples/debugging/fastqc/fastqc_blog.cwl
new file mode 100644 (file)
index 0000000..340c1ec
--- /dev/null
+++ b/blog-examples/debugging/fastqc/fastqc_blog.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/fastqc/fastqc_blog.yml b/blog-examples/debugging/fastqc/fastqc_blog.yml
new file mode 100644 (file)
index 0000000..0c56a57
--- /dev/null
+++ b/blog-examples/debugging/fastqc/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/fastqc/fastqc_blog_broken.cwl b/blog-examples/debugging/fastqc/fastqc_blog_broken.cwl
new file mode 100644 (file)
index 0000000..8d3d348
--- /dev/null
+++ b/blog-examples/debugging/fastqc/fastqc_blog_broken.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: Files
+    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/fastqc/fastqc_blog_mismatch.yml b/blog-examples/debugging/fastqc/fastqc_blog_mismatch.yml
new file mode 100644 (file)
index 0000000..6441654
--- /dev/null
+++ b/blog-examples/debugging/fastqc/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

diff --git a/blog-examples/debugging/star-index/.gitignore b/blog-examples/debugging/star-index/.gitignore
new file mode 100644 (file)
index 0000000..681307f
--- /dev/null
+++ b/blog-examples/debugging/star-index/.gitignore
@@ -0,0 +1 @@
+rnaseq

diff --git a/blog-examples/debugging/star-index/README.md b/blog-examples/debugging/star-index/README.md
new file mode 100644 (file)
index 0000000..70872ac
--- /dev/null
+++ b/blog-examples/debugging/star-index/README.md
@@ -0,0 +1,16 @@
+
+To test this:
+
+  mkdir rnaseq
+  cd rnaseq
+  wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/
+  cd ..
+
+Then:
+
+   arvados-cwl-runner STAR-index-broken.cwl STAR-index.yml
+
+or:
+
+   arvados-cwl-runner STAR-index.cwl STAR-index.yml
+

diff --git a/blog-examples/debugging/star-index/STAR-index-broken.cwl b/blog-examples/debugging/star-index/STAR-index-broken.cwl
new file mode 100755 (executable)
index 0000000..10b3fa1
--- /dev/null
+++ b/blog-examples/debugging/star-index/STAR-index-broken.cwl
@@ -0,0 +1,58 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
+
+inputs:
+
+  InputFiles:
+    format: http://edamontology.org/format_1930
+    type: File[]
+    inputBinding:
+      prefix: "--genomeFastaFiles"
+
+  IndexName:
+    type: string
+    inputBinding:
+      prefix: "--genomeDir"
+      valueFrom: ./$(self)
+
+#Optional Inputs
+
+  Gtf:
+    type: File?
+    inputBinding:
+      prefix: "--sjdbGTFfile"
+
+  Overhang:
+    type: int?
+    inputBinding:
+      prefix: "--sjdbOverhang"
+
+  Junctions:
+    type: File?
+    inputBinding:
+      prefix: "--sjdbFileChrStartEnd"
+
+  GenomeSize:
+    type: int?
+    inputBinding:
+      prefix: "--genomeSAindexNbases"
+
+  GenomeBits:
+    type: int?
+    inputBinding:
+      prefix: "--genomeChrBinNbits"
+
+baseCommand: [STAR, --runMode, genomeGenerate]
+
+arguments: [--runThreadN, $(runtime.cores)]
+
+outputs:
+  indexes:
+    type: Directory
+    outputBinding:
+      glob: ./$(inputs.IndexName)/

diff --git a/blog-examples/debugging/star-index/STAR-index.cwl b/blog-examples/debugging/star-index/STAR-index.cwl
new file mode 100755 (executable)
index 0000000..74ee7db
--- /dev/null
+++ b/blog-examples/debugging/star-index/STAR-index.cwl
@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
+  ResourceRequirement:
+    coresMin: 2
+    ramMin: 12000
+
+inputs:
+
+  InputFiles:
+    format: http://edamontology.org/format_1930
+    type: File[]
+    inputBinding:
+      prefix: "--genomeFastaFiles"
+
+  IndexName:
+    type: string
+    inputBinding:
+      prefix: "--genomeDir"
+      valueFrom: ./$(self)
+
+#Optional Inputs
+
+  Gtf:
+    type: File?
+    inputBinding:
+      prefix: "--sjdbGTFfile"
+
+  Overhang:
+    type: int?
+    inputBinding:
+      prefix: "--sjdbOverhang"
+
+  Junctions:
+    type: File?
+    inputBinding:
+      prefix: "--sjdbFileChrStartEnd"
+
+  GenomeSize:
+    type: int?
+    inputBinding:
+      prefix: "--genomeSAindexNbases"
+
+  GenomeBits:
+    type: int?
+    inputBinding:
+      prefix: "--genomeChrBinNbits"
+
+baseCommand: [STAR, --runMode, genomeGenerate]
+
+arguments: [--runThreadN, $(runtime.cores)]
+
+outputs:
+  indexes:
+    type: Directory
+    outputBinding:
+      glob: ./$(inputs.IndexName)/

diff --git a/blog-examples/debugging/star-index/STAR-index.yml b/blog-examples/debugging/star-index/STAR-index.yml
new file mode 100644 (file)
index 0000000..189faf2
--- /dev/null
+++ b/blog-examples/debugging/star-index/STAR-index.yml
@@ -0,0 +1,9 @@
+InputFiles:
+  - class: File
+    location: rnaseq/reference_data/chr1.fa
+    format: http://edamontology.org/format_1930
+IndexName: 'hg19-chr1-STAR-index'
+Gtf:
+  class: File
+  location: rnaseq/reference_data/chr1-hg19_genes.gtf
+Overhang: 99