+++ /dev/null
-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
-
+++ /dev/null
-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)
+++ /dev/null
-fastq1:
- class: Directory
- location: keep:c96565a96cd428fe92bf70e97488bd80+21857
-
-fastq2:
- class: File
- location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
-
fastq1:
type: File
label: One of set of pair-end FASTQs (R1)
-
+
fastq2:
type: File
label: One of set of pair-end FASTQs (R2)
--- /dev/null
+fastq1:
+ class: File
+ location: keep:be73607762d9948f8da2c1151dc3ef46+70694/ERR2122553_1.fastq.gz
+
+fastq2:
+ class: File
+ location: keep:be73607762d9948f8da2c1151dc3ef46+70694/ERR2122553_2.fastq.gz
requirements:
DockerRequirement:
dockerPull: biocontainers/fastqc:v0.11.9_cv6
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.fastq1)
+ - $(inputs.fastq2)
hints:
SoftwareRequirement:
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)
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
--- /dev/null
+fastq1:
+ class: Directory
+ location: keep:be73607762d9948f8da2c1151dc3ef46+70694
+
+fastq2:
+ class: File
+ location: keep:be73607762d9948f8da2c1151dc3ef46+70694/ERR2122553_2.fastq.gz