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")
