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mr-c/novice-tutorial.cwl

Created October 4, 2022 15:03
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novice-tutorial.cwl
{
"$graph": [
{
"class": "Workflow",
"requirements": [
{
"class": "MultipleInputFeatureRequirement"
}
],
"inputs": [
{
"type": "File",
"format": "https://edamontology.org/format_1930",
"id": "#main/rna_reads_forward"
},
{
"type": "File",
"format": "https://edamontology.org/format_1930",
"id": "#main/rna_reads_reverse"
}
],
"steps": [
{
"run": "#multiqc.cwl",
"in": [
{
"source": [
"#main/quality_control_forward/zipped_file",
"#main/quality_control_reverse/zipped_file"
],
"id": "#main/combine_reports/qc_files_array"
}
],
"out": [
"#main/combine_reports/multiqc_html"
],
"id": "#main/combine_reports"
},
{
"run": "#fastqc_2.cwl",
"in": [
{
"source": "#main/rna_reads_forward",
"id": "#main/quality_control_forward/reads_file"
}
],
"out": [
"#main/quality_control_forward/zipped_file"
],
"id": "#main/quality_control_forward"
},
{
"run": "#fastqc_2.cwl",
"in": [
{
"source": "#main/rna_reads_reverse",
"id": "#main/quality_control_reverse/reads_file"
}
],
"out": [
"#main/quality_control_reverse/zipped_file"
],
"id": "#main/quality_control_reverse"
}
],
"id": "#main",
"outputs": [
{
"type": "File",
"outputSource": "#main/combine_reports/multiqc_html",
"id": "#main/combined_quality_report"
}
]
},
{
"class": "CommandLineTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"hints": [
{
"class": "LoadListingRequirement",
"loadListing": "deep_listing"
},
{
"class": "NetworkAccess",
"networkAccess": true
},
{
"class": "DockerRequirement",
"dockerPull": "biowardrobe2/fastqc:v0.11.5"
},
{
"class": "SoftwareRequirement",
"packages": [
{
"specs": [
"http://identifiers.org/biotools/fastqc"
],
"version": [
"0.1.11.5"
],
"package": "fastqc"
}
]
}
],
"inputs": [
{
"type": [
"File"
],
"inputBinding": {
"position": 50
},
"doc": "Input bam,sam,bam_mapped,sam_mapped or fastq file\n",
"id": "#fastqc_2.cwl/reads_file"
}
],
"outputs": [
{
"type": [
"File"
],
"outputBinding": {
"glob": "*.html"
},
"id": "#fastqc_2.cwl/html_file"
},
{
"type": [
"File"
],
"outputBinding": {
"glob": "${\n return \"*/summary.txt\";\n}\n"
},
"id": "#fastqc_2.cwl/summary_file"
},
{
"type": [
"File"
],
"outputBinding": {
"glob": "*.zip"
},
"id": "#fastqc_2.cwl/zipped_file"
}
],
"baseCommand": [
"fastqc",
"--extract",
"--outdir",
"."
],
"doc": "Tool runs FastQC from Babraham Bioinformatics\n",
"id": "#fastqc_2.cwl",
"http://schema.org/name": "fastqc_2",
"http://schema.org/license": "http://www.apache.org/licenses/LICENSE-2.0",
"http://schema.org/isPartOf": {
"class": "http://schema.org/CreativeWork",
"http://schema.org/name": "Common Workflow Language",
"http://schema.org/url": "http://commonwl.org/"
},
"http://schema.org/creator": [
{
"class": "http://schema.org/Organization",
"http://schema.org/legalName": "Cincinnati Children's Hospital Medical Center",
"http://schema.org/location": [
{
"class": "http://schema.org/PostalAddress",
"http://schema.org/addressCountry": "USA",
"http://schema.org/addressLocality": "Cincinnati",
"http://schema.org/addressRegion": "OH",
"http://schema.org/postalCode": "45229",
"http://schema.org/streetAddress": "3333 Burnet Ave",
"http://schema.org/telephone": "+1(513)636-4200"
}
],
"http://schema.org/logo": "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png",
"http://schema.org/department": [
{
"class": "http://schema.org/Organization",
"http://schema.org/legalName": "Allergy and Immunology",
"http://schema.org/department": [
{
"class": "http://schema.org/Organization",
"http://schema.org/legalName": "Barski Research Lab",
"http://schema.org/member": [
{
"class": "http://schema.org/Person",
"http://schema.org/name": "Michael Kotliar",
"http://schema.org/email": "mailto:misha.kotliar@gmail.com",
"http://schema.org/sameAs": [
{
"id": "#0000-0002-6486-3898"
}
]
}
]
}
]
}
]
}
]
},
{
"class": "CommandLineTool",
"doc": "Run multiqc on log files from supported bioinformatic tools.\n26/04/2020: Fixed output filenames, added support for a single input file in qc_files_array (Miguel Boland)\n",
"requirements": [
{
"listing": "${// script merges the to input arrays\n // into one array that fulfills the type \n // requirement for \"listing\", which is\n // \"{type: array, items: [File, Directory]}\"\n\n var qc_files_array = inputs.qc_files_array;\n var qc_files_array_of_array = null; # inputs.qc_files_array_of_array;\n var output_array = [];\n\n // add items of the qc_files_array to the output_array\n if ( qc_files_array != null ){\n // Fix to allow single qc_file_array\n if (qc_files_array.length === undefined){\n output_array.push(qc_files_array)\n } else {\n for (var i=0; i<qc_files_array.length; i++){\n output_array.push(qc_files_array[i])\n }\n\n }\n }\n\n // add items of the qc_files_array_of_array to the output_array\n if ( qc_files_array_of_array != null ){\n for (var i=0; i<qc_files_array_of_array.length; i++){ \n for (var ii=0; ii<qc_files_array_of_array[i].length; ii++){\n output_array.push(qc_files_array_of_array[i][ii])\n }\n }\n }\n\n return output_array\n}\n",
"class": "InitialWorkDirRequirement"
},
{
"class": "InlineJavascriptRequirement"
}
],
"hints": [
{
"class": "LoadListingRequirement",
"loadListing": "deep_listing"
},
{
"class": "NetworkAccess",
"networkAccess": true
},
{
"dockerPull": "kerstenbreuer/multiqc:1.7",
"class": "DockerRequirement"
},
{
"coresMin": 1,
"ramMin": 10000,
"class": "ResourceRequirement"
}
],
"baseCommand": [
"multiqc"
],
"arguments": [
{
"valueFrom": "--zip-data-dir",
"position": 1
},
{
"valueFrom": "'log_filesize_limit: 100000000'",
"position": 1,
"prefix": "--cl_config"
},
{
"valueFrom": "$(runtime.outdir)",
"position": 2,
"prefix": "--outdir"
},
{
"valueFrom": "$(runtime.outdir)",
"position": 4
},
{
"prefix": "--filename",
"valueFrom": "multiqc",
"position": 3
}
],
"inputs": [
{
"doc": "qc files which shall be part of the multiqc summary;\noptional, only one of qc_files_array or qc_files_array_of_array \nmust be provided\n",
"type": [
"null",
"File",
{
"type": "array",
"items": "File"
}
],
"id": "#multiqc.cwl/qc_files_array"
}
],
"outputs": [
{
"type": "Directory",
"outputBinding": {
"glob": "."
},
"id": "#multiqc.cwl/diree"
},
{
"type": "File",
"outputBinding": {
"glob": "mulitqc.html"
},
"id": "#multiqc.cwl/multiqc_html"
},
{
"type": "File",
"outputBinding": {
"glob": "multiqc_data.zip"
},
"id": "#multiqc.cwl/multiqc_zip"
}
],
"id": "#multiqc.cwl"
}
],
"cwlVersion": "v1.2",
"$schemas": [
"https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf"
]
}
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