class Outputs(define.Outputs): Out_raw_vcf = define.output(name="Raw vcf output", description="Raw vcf file.", required=False, list=False) Out_recalFile = define.output( name="Output recal file", description="The output recal file used by ApplyRecalibration.", required=False, list=False) Out_tranchesFile = define.output( name="Output tranches file", description="The output tranches file used by ApplyRecalibration.", required=False, list=False) Out_rscriptFile = define.output( name="Output rscript file", description= "The output rscript file generated by the VQSR to aid in visualization of the input data and learned model.", required=False, list=False) Out_vcf = define.output(name="Filtered VCF file", description="Filtered VCF file.", required=False, list=False)
class Outputs(define.Outputs): dedup_realn_bam = define.output(description="Dedup Realn BAM", required=True, list=True) dedup_realn_bai = define.output(description="Dedup Realn BAM Index", required=True, list=True)
class Outputs(define.Outputs): #dedup_realn_bam_grp = define.output(description="Dedup Realn BAM Group", required=True) grp = define.output( name="Recalibration Table Output", description="The output recalibration table file to create", required=True, list=False) #, alt_path='/extra'
class Outputs(define.Outputs): out = define.output( name='File to write the output to.', description="Files(s) containing summary alignment metrics.")
class Outputs(define.Outputs): out = define.output(description="SNP Output VCF")
class Outputs(define.Outputs): out = define.output(name='Aligned SAM or BAM file', description="SAM or BAM Files(s) after sorting") out_bai = define.output(name='BAM index file', description="Bai file")
class Outputs(define.Outputs): dedup_bam_intervals = define.output(description="Dedup BAM Intervals", required=True, list=True) # , alt_path='/extra'
class Outputs(define.Outputs): all_vcf = define.output(description="Output VCF", list=True, required=True) #, alt_path='/extra'
class Outputs(define.Outputs): out = define.output(description="Merged VCF", required=True)
class Outputs(define.Outputs): out = define.output(name="Output BAM file", list=True, required=True) #, alt_path='/extra' bai = define.output(name="Output BAI file", list=True, required=True)
class Outputs(define.Outputs): out = define.output(name='output VCF file', description="Filtered VCF")
class Outputs(define.Outputs): out = define.output(name = 'Merged BAM/SAM files', description = "Merged BAM/SAM files" ) ind = define.output(name = 'Index file', alt_path='/extra' )
class Outputs(define.Outputs): out_fq = define.output(name="Filtered FASTQ files",list =True, description="FASTQ files processed according to the set parameters") out_skip = define.output(name="Skipped Reads",list =True, description="FASTQ files containing reads that were filtered out from the input") out_summary = define.output(name="Summary", description="A text file containing summary of the filtration")