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dxapp.json
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dxapp.json
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{
"name": "fastqc_v1.4.0",
"title": "FastQC Reads Quality Control v1.4.0",
"summary": "v1.4.0 - Generates a QC report on reads data",
"tags": [
"Read QC",
"Statistics"
],
"properties": {
"github release": "v1.4.0"
},
"dxapi": "1.0.0",
"inputSpec": [
{
"name": "reads",
"label": "Reads",
"help": "one or more files containing the reads to be checked. Accepted formats are gzipped-FASTQ and BAM.",
"class": "array:file",
"patterns": ["*.fq.gz", "*.fastq.gz", "*.sam", "*.bam"]
},
{
"name": "contaminants_txt",
"label": "Custom contaminants",
"help": "A special file containing custom contaminant sequences to screen overrepresented sequences against. If left empty, a default set of contaminants that comes with the FastQC package will be used. If provided, this file must be a text file with two tab-delimited columns: name (such as 'Truseq Adapter') and DNA sequence (such as 'TATCTCGTATG').",
"class": "file",
"patterns": ["*.fastqc_contaminants.txt"],
"optional": true
},
{
"name": "adapters_txt",
"label": "Custom adapters",
"help": "A special file containing custom adapter sequences which will be explicity searched against the library. If left empty, a default set of adapters that comes with the FastQC package will be used. If provided, this file must be a text file with two tab-delimited columns: name (such as 'Nextera Transposase Sequence') and DNA sequence (such as 'CTGTCTCTTATA').",
"class": "file",
"patterns": ["*.fastqc_adapters.txt"],
"optional": true
},
{
"name": "limits_txt",
"label": "Custom limits",
"help": "A special file containing a set of criteria which will be used to determine the warn/error limits for the various modules, or selectively remove some modules from the output altogether. For an example of a limits file, refer to the limits.txt file in the FastQC sources.",
"class": "file",
"patterns": ["*.fastqc_limits.txt"],
"optional": true
},
{
"name": "format",
"label": "Input format",
"help": "The format of the input file. By default FastQC will try to automatically detect the format based on the input filename. You can override this by choosing a specific format (fastq, bam, or bam_mapped). For BAM files, choose bam if you want all the entries to be processed, or bam_mapped if you want only the mapped entries to be processed.",
"class": "string",
"default": "auto",
"choices": [
"auto",
"fastq",
"bam",
"bam_mapped"
],
"group": "Advanced"
},
{
"name": "kmer_size",
"label": "Kmer size",
"help": "The kmer size that the kmer analysis module will use. This module reports overrepresented k-mers (sequences of size 'k'). This size must be between 2 and 10 (default is 7).",
"class": "int",
"default": 7,
"group": "Advanced"
},
{
"name": "nogroup",
"label": "Disable grouping of bases past 50bp?",
"help": "Disable grouping of bases for reads >50bp. All reports will show data for every base in the read. WARNING: Using this option may cause fastqc to slow down or crash if used on really long reads, and resulting plots may be too large for practical viewing.",
"class": "boolean",
"default": true,
"group": "Advanced"
},
{
"name": "extra_options",
"label": "Extra command-line options",
"help": "Extra command-line options that will be passed directly to the fastqc invocation. Example: --nofilter",
"class": "string",
"optional": true,
"group": "Advanced"
}
],
"outputSpec": [
{
"name": "report_html",
"label": "FastQC Report",
"help": "An html file archive containing the report as generated by FastQC.",
"class": "array:file",
"patterns": ["*.stats-fastqc.html"]
},
{
"name": "stats_txt",
"label": "FastQC Stats",
"help": "A text file containing the machine-readable statistics as generated by FastQC.",
"class": "array:file",
"patterns": ["*.stats-fastqc.txt"]
}
],
"runSpec": {
"execDepends": [],
"file": "src/code.sh",
"release": "20.04",
"version": "0",
"interpreter": "bash",
"distribution": "Ubuntu"
},
"access": {
"network": [
"*"
],
"project": "CONTRIBUTE",
"allProjects": "VIEW"
},
"ignoreReuse": false,
"regionalOptions": {
"aws:us-east-1": {
"systemRequirements": {
"main": {
"instanceType": "mem1_ssd1_v2_x2"
}
}
}
}
}