X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/5b4f2a85bedfad9e72e406e3e1990afc913c9da2..bec60d8f8671fedf159d9be0c02196ebaf602d53:/RNA-Seq/cwl/helper/fastqc_2.cwl

diff --git a/RNA-Seq/cwl/helper/fastqc_2.cwl b/RNA-Seq/cwl/helper/fastqc_2.cwl
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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1
+  SoftwareRequirement:
+    packages:
+      fastqc:
+        specs: [ "http://identifiers.org/biotools/fastqc" ]
+        version: [ "0.11.9--hdfd78af_1", "0.11.9" ]
+
+inputs:
+
+  reads_file:
+    type: File
+    inputBinding:
+      position: 50
+    doc: |
+      Input bam,sam,bam_mapped,sam_mapped or fastq file
+
+  format_enum:
+    type:
+      - "null"
+      - type: enum
+        name: "format"
+        symbols: ['bam','sam','bam_mapped','sam_mapped','fastq']
+    inputBinding:
+      position: 6
+      prefix: '--format'
+    doc: |
+      Bypasses the normal sequence file format detection and
+      forces the program to use the specified format.  Valid
+      formats are bam,sam,bam_mapped,sam_mapped and fastq
+
+  threads:
+    type: int?
+    inputBinding:
+      position: 7
+      prefix: '--threads'
+    doc: |
+      Specifies the number of files which can be processed
+      simultaneously.  Each thread will be allocated 250MB of
+      memory so you shouldn't run more threads than your
+      available memory will cope with, and not more than
+      6 threads on a 32 bit machine
+
+  contaminants:
+    type: File?
+    inputBinding:
+      position: 8
+      prefix: '--contaminants'
+    doc: |
+      Specifies a non-default file which contains the list of
+      contaminants to screen overrepresented sequences against.
+      The file must contain sets of named contaminants in the
+      form name[tab]sequence.  Lines prefixed with a hash will
+      be ignored.
+
+  adapters:
+    type: File?
+    inputBinding:
+      position: 9
+      prefix: '--adapters'
+    doc: |
+      Specifies a non-default file which contains the list of
+      adapter sequences which will be explicity searched against
+      the library. The file must contain sets of named adapters
+      in the form name[tab]sequence.  Lines prefixed with a hash
+      will be ignored.
+
+  limits:
+    type: File?
+    inputBinding:
+      position: 10
+      prefix: '--limits'
+    doc: |
+      Specifies a non-default file which contains a set of criteria
+      which will be used to determine the warn/error limits for the
+      various modules.  This file can also be used to selectively
+      remove some modules from the output all together.  The format
+      needs to mirror the default limits.txt file found in the
+      Configuration folder.
+
+  kmers:
+    type: int?
+    inputBinding:
+      position: 11
+      prefix: '--kmers'
+    doc: |
+      Specifies the length of Kmer to look for in the Kmer content
+      module. Specified Kmer length must be between 2 and 10. Default
+      length is 7 if not specified.
+
+  casava:
+    type: boolean?
+    inputBinding:
+      position: 13
+      prefix: '--casava'
+    doc: |
+      Files come from raw casava output. Files in the same sample
+      group (differing only by the group number) will be analysed
+      as a set rather than individually. Sequences with the filter
+      flag set in the header will be excluded from the analysis.
+      Files must have the same names given to them by casava
+      (including being gzipped and ending with .gz) otherwise they
+      won't be grouped together correctly.
+
+  nofilter:
+    type: boolean?
+    inputBinding:
+      position: 14
+      prefix: '--nofilter'
+    doc: |
+      If running with --casava then don't remove read flagged by
+      casava as poor quality when performing the QC analysis.
+
+  hide_group:
+    type: boolean?
+    inputBinding:
+      position: 15
+      prefix: '--nogroup'
+    doc: |
+      Disable grouping of bases for reads >50bp. All reports will
+      show data for every base in the read.  WARNING: Using this
+      option will cause fastqc to crash and burn if you use it on
+      really long reads, and your plots may end up a ridiculous size.
+      You have been warned!
+
+outputs:
+
+  zipped_file:
+    type: File
+    outputBinding:
+      glob: '*.zip'
+  html_file:
+    type: File
+    outputBinding:
+      glob: '*.html'
+  summary_file:
+    type: File
+    outputBinding:
+      glob: "*/summary.txt"
+
+baseCommand: [fastqc, --extract, --outdir, .]
+
+$namespaces:
+  s: http://schema.org/
+
+$schemas:
+- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
+
+s:name: "fastqc_2"
+s:license: http://www.apache.org/licenses/LICENSE-2.0
+
+s:creator:
+- class: s:Organization
+  s:legalName: "Cincinnati Children's Hospital Medical Center"
+  s:location:
+  - class: s:PostalAddress
+    s:addressCountry: "USA"
+    s:addressLocality: "Cincinnati"
+    s:addressRegion: "OH"
+    s:postalCode: "45229"
+    s:streetAddress: "3333 Burnet Ave"
+    s:telephone: "+1(513)636-4200"
+  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
+  s:department:
+  - class: s:Organization
+    s:legalName: "Allergy and Immunology"
+    s:department:
+    - class: s:Organization
+      s:legalName: "Barski Research Lab"
+      s:member:
+      - class: s:Person
+        s:name: Michael Kotliar
+        s:email: mailto:misha.kotliar@gmail.com
+        s:sameAs:
+        - id: http://orcid.org/0000-0002-6486-3898
+
+doc: |
+  Tool runs FastQC from Babraham Bioinformatics