SRAlign/parameter_specifications.json at main · trev-f/SRAlign · GitHub

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{
    "mandatory" : {
        "title" : "Mandatory parameters",
        "parameters" : {
            "input"  : {
                "description" : "Path to input csv file."
            },
            "genome" : {
                "description" : "Reference genome ID."
            }
        }
    },
    "io" : {
        "title" : "Input/Output parameters",
        "parameters" : {
            "baseDirGenome" : {
                "default"     : "${launchDir}/data/references",
                "description" : "Path to base directory where genomes are found."
            },
            "baseDirReport" : {
                "default"     : "${launchDir}/results/reports",
                "description" : "Path to base directory where output reports will be stored."
            },
            "baseDirData"   : {
                "default"     : "${launchDir}/results/data",
                "description" : "Path to base directory where output data will be stored."
            }
        }
    },
    "reportQC" : {
        "title" : "QC reporting parameters",
        "parameters" : {
            "multiqcConfig" : {
                "default"     : "${projectDir}/configs/full_multiqc_config.yaml",
                "description" : "Path to MultiQC config file."
            }
        }
    },
    "references" : {
        "title" : "Reference parameters",
        "parameters" : {
            "contaminant"   : {
                "default"     : "EB1",
                "description" : "Contaminant genome ID."
            }
        }
    },
    "readsQC"   : {
        "title" : "Reads QC parameters",
        "parameters" : {
            "skipReadsQC"   : {
                "default"     : false,
                "description" : "Skip all reporting of reads QC. This skips FastQC reporting for raw and trimmed reads as well as the creation of a dedicated reads MultiQC report."
            },
            "skipDedicatedReadsMultiQC"   : {
                "default"     : false,
                "description" : "Skip creation of an additional MultiQC report for reads. FastQC metrics will still be present in the final MultiQC report upon pipeline completion. A dedicated reads MultiQC report can be beneficial for assessing information about reads prior to (or concurrent with) alignment and post-alignment steps."
            },
            "skipRawFastQC" : {
                "default"     : false,
                "description" : "Skip FastQC report for raw reads."
            }
        }
    },
    "trimReads" : {
        "title" : "Read-trimming parameters",
        "parameters" : {
            "trimTool"      : {
                "default"     : "fastp",
                "description" : "Tool to use for read trimming."
            },
            "adapterR1"     : {
                "default"     : "",
                "description" : "Adapter sequence to trim from read 1."
            },
            "adapterR2"     : {
                "default"     : "",
                "description" : "Adapter sequence to trim from read 2."
            },
            "skipTrimReads" : {
                "default"     : false,
                "description" : "Skip the read trimming step.",
                "skip"        : true
            },
            "skipTrimFastQC" : {
                "default"     : false,
                "description" : "Skip QC report for trimmed reads.",
                "skip"        : true
            }
        }
    },
    "alignment" : {
        "title" : "Alignment parameters",
        "parameters" : {
            "alignmentTool" : {
                "default"     : "bowtie2",
                "description" : "Tool to use for alignment to reference. The same tool is used to align to both genome and contaminant."
            },
            "forceAlignRawReads" : {
                "default"     : false,
                "description" : "Force alignment of raw reads even if read trimming is performed."
            },
            "forceUseHisat2Index" : {
                "default"     : true,
                "description" : "Use the provided HISAT2 index if it is supplied."
            },
            "buildSpliceAwareIndex" : {
                "default"     : false,
                "description" : "Build the alignment tool index in a splice-aware manner (for aligners where this is possible)."
            },
            "skipAlignGenome" : {
                "default"     : false,
                "description" : "Skip alignment of reads to reference.",
                "skip"        : true
            },
            "skipAlignContam" : {
                "default"     : false,
                "description" : "Skip alignment of reads to contaminant.",
                "skip"        : true
            }
        }
    },
    "libraryQC" : {
        "title" : "Library QC parameters",
        "parameters" : {
            "skipAlignmentStatsQC" : {
                "default"     : false,
                "description" : "Skip QC report for alignment.",
                "skip"        : true
            }
        }
    },
    "libraryComplexity" : {
        "title" : "Library complexity parameters",
        "parameters" : {
            "skipPreseq"    : {
                "default"     : false,
                "description" : "Skip Preseq.",
                "skip"        : true
            }
        }
    },
    "resources" : {
        "title" : "Resources default parameters",
        "parameters" : {
            "maxCpus"       : {
                "default"     : 16,
                "description" : "Maximum number of CPUs for a task."
            },
            "maxMemory"     : {
                "default"     : "24.GB",
                "description" : "Maximum memory for a task."
            },
            "maxTime"       : {
                "default"     : "24.h",
                "description" : "Maximum time for a task."
            }
        }
    },
    "miscellaneous" : {
        "title" : "Miscellaneous parameters",
        "parameters" : {
            "seed"          : {
                "default"     : 40,
                "description" : "Seed integer for all pseudo-random processes. Specific seed value should not be important but ensures reproducibility."
            },
            "help"          : {
                "default"     : null,
                "description" : "Display this help message and exit the program."
            }
        }
    }
}