--- /dev/null
+#!/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
projects / arvados-tutorial.git / blobdiff