From ec904dcdfc5ace2774af00636890f2e6f403839b Mon Sep 17 00:00:00 2001 From: Ward Vandewege Date: Wed, 24 Nov 2021 09:47:18 -0500 Subject: [PATCH] 18178: Final tweaks to the debugging blog post CWL. Arvados-DCO-1.1-Signed-off-by: Ward Vandewege --- .../debugging/fastq_example/fastqc_blog.yml | 8 ----- .../fastq_example/fastqc_blog_broken.cwl | 29 ------------------- .../fastq_example/fastqc_blog_mismatch.yml | 8 ----- .../fastqc_blog.cwl} | 2 +- .../debugging/fastqc_example/fastqc_blog.yml | 7 +++++ .../fastqc_blog_broken.cwl} | 11 +++++-- .../fastqc_example/fastqc_blog_mismatch.yml | 7 +++++ 7 files changed, 23 insertions(+), 49 deletions(-) delete mode 100644 blog-examples/debugging/fastq_example/fastqc_blog.yml delete mode 100644 blog-examples/debugging/fastq_example/fastqc_blog_broken.cwl delete mode 100644 blog-examples/debugging/fastq_example/fastqc_blog_mismatch.yml rename blog-examples/debugging/{fastq_example/fastqc_blog_fixed.cwl => fastqc_example/fastqc_blog.cwl} (99%) create mode 100644 blog-examples/debugging/fastqc_example/fastqc_blog.yml rename blog-examples/debugging/{fastq_example/fastqc_blog.cwl => fastqc_example/fastqc_blog_broken.cwl} (84%) create mode 100644 blog-examples/debugging/fastqc_example/fastqc_blog_mismatch.yml 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 -- 2.30.2