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modules.config
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80 lines (79 loc) · 2.46 KB
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/*
* -------------------------------------------------
* Nextflow config file for module specific-options
* -------------------------------------------------
*/
params {
modules {
'fastqc' {
args = "--quiet"
suffix = ""
publish_dir = "Reports/FastQC"
publish_results = "all"
}
'trimgalore' {
args = "--fastqc"
suffix = ""
publish_dir = "trimgalore"
publish_results = "all"
}
'bwa_index' {
args = ""
suffix = ""
publish_dir = "genome/bwa_index"
publish_results = "all"
}
'bwa_mem' {
args = "-K 100000000 -M"
args2 = ""
extra = ""
suffix = ""
publish_dir = ""
publish_results = "all"
}
'bwamem2_index' {
args = ""
suffix = ""
publish_dir = "genome/bwa_index"
publish_results = "all"
}
'bwamem2_mem' {
args = "-K 100000000 -M"
args2 = ""
extra = ""
suffix = ""
publish_dir = ""
publish_results = "all"
}
'samtools_index_mapped' {
args = ""
suffix = ""
publish_dir = "Mapped"
publish_results = "all"
}
'samtools_index_recal' {
args = ""
suffix = "recal"
publish_dir = ""
publish_results = "all"
}
'gatk_markduplicates' {
args = "ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
suffix = ".mLb.mkD"
publish_dir = "bwa/mergedLibrary"
publish_results = "all"
}
'get_software_versions' {
args = ""
suffix = ""
publish_dir = "pipeline_info"
publish_results = "all"
}
'output_documentation' {
args = ""
suffix = ""
publish_dir = "pipeline_info"
publish_results = "all"
}
}
}