def indexRefbwa(inputs, outputs):
"""
Index reference file for use with BWA.
"""
ref = inputs
flagFile = outputs
runStageCheck('indexReferenceBWA', flagFile, ref)
def fastqc(inputs, outputs):
"""
Run FastQC on each fastq file.
"""
sequence = inputs
fastqc_dest, flagFile = outputs
runStageCheck('fastqc', flagFile, fastqc_dir, sequence)
def tumour_sam_to_bam(inputs, outputs):
samFile, _success = inputs
bamFile, flagFile = outputs
match = re.search('(.*)\.sam', samFile)
bamFile = match.group(1) + '.bam'
runStageCheck('tumour_sam_to_bam', flagFile, samFile, bamFile)
def simulate_variants(inputs, outputs):
variant_fasta, _success = inputs
fasta_out, flagFile = outputs
match = re.search('(.*)\/([a-zA-Z0-9_\.]+)\.fa', variant_fasta)
variant_fasta = '%s/%s' % (match.group(1), match.group(2))
runStageCheck('simulate_variants', flagFile, javasim_libdir,
javasim_bindir, ref_fasta, variant_fasta)
def tumour_sort_bam(inputs, outputs):
bamFile, _success = inputs
sortBamFile, flagFile = outputs
match = re.search('(.*)\.bam', bamFile)
sortBamPrefix = match.group(1) + '.sorted.bam'
runStageCheck('tumour_sort_bam', flagFile, bamFile, sortBamPrefix)
def fastqc_trimmed(inputs, outputs):
"""
Run FastQC on each trimmed paired fastq file.
"""
sequence = inputs
fastqc_dest, flagFile = outputs
runStageCheck('fastqc', flagFile, fastqc_dir, sequence)
def indexRefSamtools(inputs, outputs):
"""
Index reference file for use with samtools.
"""
ref = inputs
out, flagFile = outputs
runStageCheck('indexReferenceSAM', flagFile, ref)
def igvcountDedupedBams(inputs, outputs):
"""
Use igvtools count to create a .tdf file for the deduped bam files, to improve viewing of the bam coverage in igv. Note that this actually goes from the fixMate-ed bams.
"""
bam, _success = inputs
outfile, flag_file = outputs
print "igvtools count on %s" % os.path.basename(bam)
runStageCheck('igvcount', flag_file, bam, outfile)
def vcfIndexIndels(inputs, outputs):
"""
Use bgzip and tabix to prepare raw indels vcf for vcftools handling.
"""
vcf, _idx, _success = inputs
zipfile, tabix_index, flag_file = outputs
print "bgzip and tabix (for vcftools) on %s" % vcf
runStageCheck('indexVCF', flag_file, vcf)
def igvcountRecalibratedBams(inputs, outputs):
"""
Use igvtools count to create a .tdf file for the recalibrated bam files, to improve viewing of the bam coverage in igv.
"""
bam, _success = inputs
outfile, flag_file = outputs
print "igvtools count on %s" % os.path.basename(bam)
runStageCheck('igvcount', flag_file, bam, outfile)
def igvcountDedupedBams(inputs, outputs):
"""
Use igvtools count to create a .tdf file for the deduped bam files, to improve viewing of the bam coverage in igv. Note that this actually goes from the fixMate-ed bams.
"""
bam, _success = inputs
outfile, flag_file = outputs
print "igvtools count on %s" % os.path.basename(bam)
runStageCheck('igvcount', flag_file, bam, outfile)
def indexRealignedBams(inputs, outputs):
"""
Index the locally realigned bams using samtools.
"""
bam, _success = inputs
output, flag_file = outputs
print "samtools index on %s" % os.path.basename(bam)
runStageCheck('indexBam', flag_file, bam)
def indexRealignedBams(inputs, outputs):
"""
Index the locally realigned bams using samtools.
"""
bam = inputs
output, flag_file = outputs
print "samtools index on %s" % os.path.basename(bam)
runStageCheck('indexBam', flag_file, bam)
def vcfIndexIndels(inputs, outputs):
"""
Use bgzip and tabix to prepare raw indels vcf for vcftools handling.
"""
vcf, _idx, _success = inputs
zipfile, tabix_index, flag_file = outputs
print "bgzip and tabix (for vcftools) on %s" % vcf
runStageCheck('indexVCF', flag_file, vcf)
def countRunBam(inputs, outputs):
"""
Run samtools flagstat on the initial per-lane, per-run bam file.
"""
bam, _success = inputs
output, flag_file = outputs
print "Running samtools flagstat on %s" % bam
runStageCheck('flagstat', flag_file, bam, output)
def countDedupedBam(inputs, outputs):
"""
Run samtools flagstat on the deduped bam file.
"""
bam, _success = inputs
output, flag_file = outputs
print "Running samtools flagstat on %s" % bam
runStageCheck('flagstat', flag_file, bam, output)
def cleanup(inputs, outputs):
bamIndex, _success = inputs
flagFile = outputs
tumour_base_name = '%s/%s' % (outdir, tumour_outname)
normal_base_name = '%s/%s' % (outdir, normal_outname)
runStageCheck('cleanup', flagFile, tumour_base_name, normal_base_name)
def countRunBam(inputs, outputs):
"""
Run samtools flagstat on the initial per-lane, per-run bam file.
"""
bam, _success = inputs
output, flag_file = outputs
print "Running samtools flagstat on %s" % bam
runStageCheck('flagstat', flag_file, bam, output)
def countDedupedBam(inputs, outputs):
"""
Run samtools flagstat on the deduped bam file.
"""
bam, _success = inputs
output, flag_file = outputs
print "Running samtools flagstat on %s" % bam
runStageCheck('flagstat', flag_file, bam, output)
def igvcountRecalibratedBams(inputs, outputs):
"""
Use igvtools count to create a .tdf file for the recalibrated bam files, to improve viewing of the bam coverage in igv.
"""
bam, _success = inputs
outfile, flag_file = outputs
print "igvtools count on %s" % os.path.basename(bam)
runStageCheck('igvcount', flag_file, bam, outfile)
def indexMergedBams(inputs, outputs):
"""
Index the merged bams using samtools.
"""
bam, _success = inputs
output, flag_file = outputs
print "samtools index on %s" % os.path.basename(bam)
runStageCheck('indexBam', flag_file, bam)
def indexDedupedBams(inputs, outputs):
"""
Index the de-duplicated bams using samtools. Note that this actually goes from the fixMate-ed bams.
"""
bam, _success = inputs
output, flag_file = outputs
print "samtools index on %s" % os.path.basename(bam)
runStageCheck('indexBam', flag_file, bam)
def samToBam(inputs, outputs):
"""
Convert sam to bam and sort, using Picard.
"""
output, flag_file = outputs
sam, _success = inputs
print "converting to sorted bam: %s" % os.path.basename(sam)
runStageCheck('samToSortedBam', flag_file, sam, output)
def indexDedupedBams(inputs, outputs):
"""
Index the de-duplicated bams using samtools. Note that this actually goes from the fixMate-ed bams.
"""
bam, _success = inputs
output, flag_file = outputs
print "samtools index on %s" % os.path.basename(bam)
runStageCheck('indexBam', flag_file, bam)
def indexBaseQualRecalBam(inputs, outputs):
"""
Index the locally realigned bams using samtools.
"""
bam, _baseRecalBam_success = inputs
output, flagFile = outputs
print "samtools index on %s" % bam
runStageCheck('indexBam', flagFile, bam)
def samToBam(inputs, outputs):
"""
Convert sam to bam and sort, using Picard.
"""
output, flag_file = outputs
sam, _success = inputs
print "converting to sorted bam: %s" % os.path.basename(sam)
runStageCheck('samToSortedBam', flag_file, sam, output)
def BWAmem(inputs, outputs):
"""
Align sequence reads to the reference genome using bwa mem.
"""
seq1, seq2 = inputs
output, flag_file = outputs
print "bwa mem on %s" % os.path.basename(seq1)
runStageCheck('BWAmem', flag_file, ref_files['bwa_reference'], seq1, seq2, output)
def cmh2gwas(inputs, outputs):
"""
Convert the results of the CMH test to GWAS format for viewing in IGV.
"""
test_results = inputs
gwas, flag_file = outputs
logFile = mkLogFile(logDir, test_results, '.gwas.log')
print "convert CMH results to GWAS: %s" % os.path.basename(test_results)
runStageCheck('cmh2gwas', flag_file, test_results, gwas)
def mpileuptosync(inputs,outputs):
"""
Convert mpileup to sync format for use in Popoolation2
"""
input_mpileup = inputs
output_sync, flag_file = outputs
logFile = mkLogFile(logDir, input_mpileup, '.sync.log')
print "convert from mpileup to sync format: %s" % os.path.basename(input_mpileup)
runStageCheck('mpileuptosync', flag_file, input_mpileup, output_sync)
def mpileup(inputs,outputs):
"""
Mpileup of dedupped, realigned bams - using samtools
"""
bam0, bam1, bam2, bam3, bam4, bam5, bam6, bam7, bam8, bam9 = inputs
output_mpileup, flag_file = outputs
logFile = mkLogFile(logDir, bam0, '.mpileup.log')
print "Make mpileup using Samtools: %s and other 9 files" % os.path.basename(bam0)
runStageCheck('mpileup', flag_file, ref_files['masked_reference'], bam0, bam1, bam2, bam3, bam4, bam5, bam6, bam7, bam8, bam9, output_mpileup)
def selectHighQualVariants(inputs,outputs):
"""
Select high quality variants from the initial FreeBayes variant calls to act as input for Base Quality Score Recalibration
"""
input_vcf = inputs
output_vcf, flag_file = outputs
logFile = mkLogFile(logDir, input_vcf, '.highqual.log')
print "select high quality variants using GATK SelectVariants: %s" % os.path.basename(input_vcf)
runStageCheck('selectHighQualVariants', flag_file, ref_files['fasta_reference'], input_vcf, output_vcf)
def freebayes1(inputs,outputs):
"""
First run of Freebayes, i.e. before Base Quality Score Recalibration
"""
bam0, bam1, bam2, bam3, bam4, bam5, bam6, bam7, bam8, bam9 = inputs
output_vcf, flag_file = outputs
logFile = mkLogFile(logDir, bam1, '.freebayes.log')
print "call variants using FreeBayes: %s" % os.path.basename(bam1)
runStageCheck('freebayes1', flag_file, bam0, bam1, bam2, bam3, bam4, bam5, bam6, bam7, bam8, bam9, ref_files['fasta_reference'], output_vcf)
def filterIndels(inputs, outputs):
"""
Use GATK VariantFiltration to filter raw INDEL calls.
"""
input_vcf, _idx, _success = inputs
output_vcf, _idxout, flag_file = outputs
logFile = mkLogFile(logDir, input_vcf, '.filterIndels.log')
print "filtering indels from %s" % input_vcf
runStageCheck('filterIndels', flag_file, ref_files['fasta_reference'], input_vcf, logFile, output_vcf)
def dedup(inputs, outputs):
"""
Remove apparent duplicates from merged bams using Picard MarkDuplicates.
"""
input_bam, _success = inputs
output_bam, flag_file = outputs
logFile = mkLogFile(logDir, input_bam, '.dedup.log')
print "de-duping %s" % os.path.basename(input_bam)
runStageCheck('dedup', flag_file, input_bam, logFile, output_bam)
def realignIntervals(inputs, outputs):
"""
Run GATK RealignTargetCreator to find suspect intervals for realignment.
"""
bam, _success = inputs
output_intervals, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.realignIntervals.log')
print "calculating realignment intervals for %s" % os.path.basename(bam)
runStageCheck('realignIntervals', flag_file, ref_files['fasta_reference'], bam, ref_files['indels_realign_goldstandard'], ref_files['indels_realign_1000G'], logFile, output_intervals)
def filterHapVcfs(inputs, outputs):
"""
Use GATK VariantFiltration to filter raw sample HAP calls.
"""
input_vcf, _idx, _success = inputs
output_vcf, _idxout, flag_file = outputs
logFile = mkLogFile(logDir, input_vcf, '.filterSNPs.log')
# print "filtering haplotyper vcf from %s" % input_vcf
runStageCheck('filterHapVcfs', flag_file, fasta_reference, input_vcf, logFile, output_vcf)
def callVariantRecalibrator(inputs, outputs):
"""
Use GATK VariantFiltration to filter raw SNP calls.
"""
input_vcf, _idx, _success = inputs
output_recal, output_tranches, output_R, flag_file = outputs
logFile = mkLogFile(logDir, input_vcf, '.VarRecal.log')
print "VariantRecalibrator -> %s" % input_vcf
runStageCheck('callVariantRecalibrator', flag_file, fasta_reference, input_vcf, ref_files['hapmap'],ref_files['omnimap'], ref_files['1kghc'], ref_files['dbsnp'], output_recal, output_tranches, output_R, logFile)
def callHAP(inputs, outputs):
"""
Use GATK HaplotypeCaller to call SNPs/Indels from recalibrated bams.
"""
bam, _success = inputs
output_vcf, _idx, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.callHAPs.log')
#print "calling haplotypes from %s" % bam
runStageCheck('callHAP', flag_file, fasta_reference, bam, ref_files['dbsnp'], logFile, output_vcf)
def baseQualRecalCount(inputs, outputs):
"""
GATK CountCovariates, first step of base quality score recalibration.
"""
bam, _success = inputs
output_csv, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.baseQualRecalCount.log')
print "count covariates using GATK for base quality score recalibration: %s" % os.path.basename(bam)
runStageCheck('baseQualRecalCount', flag_file, bam, ref_files['fasta_reference'], ref_files['dbsnp'], logFile, output_csv)
def callIndels(inputs, outputs):
"""
Use GATK UnifiedGenotyper to call indels from recalibrated bams.
"""
bam, _success = inputs
output_vcf, _idx, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.callIndels.log')
print "calling Indels from %s" % bam
runStageCheck('callIndels', flag_file, ref_files['fasta_reference'], bam, ref_files['dbsnp'], logFile, output_vcf)
def dedup(inputs, outputs):
"""
Remove apparent duplicates from merged bams using Picard MarkDuplicates.
"""
input_bam, _success = inputs
output_bam, flag_file = outputs
logFile = mkLogFile(logDir, input_bam, '.dedup.log')
print "de-duping %s" % os.path.basename(input_bam)
runStageCheck('dedup', flag_file, input_bam, logFile, output_bam)
def getEnsemblAnnotations(inputs, outputs):
"""
Annotate vcf using ENSEMBL variant effect predictor.
"""
vcf, _idx, _success = inputs
output, flag_file = outputs
logFile = mkLogFile(logDir, vcf, '.EnsemblAnnotation.log')
print "Annotating %s with ENSEMBL variant effect predictor" % os.path.basename(vcf)
runStageCheck('annotateEnsembl', flag_file, vcf, output, logFile)
def leftAlign(inputs,outputs):
"""
GATK LeftAlignIndels is a tool that takes a bam file and left-aligns any indels inside it
'command': "java -Xmx22g -jar " + GATK_HOME + "GenomeAnalysisTK.jar -allowPotentiallyMisencodedQuals -T LeftAlignIndels -I %input -R %ref -o %output"
"""
bam, _realign_success = inputs
output_bam, flagFile = outputs
runStageCheck('leftalignindels', flagFile, bam, fasta_reference, output_bam)
remove_GATK_bai(output_bam)
def realignIntervals(inputs, outputs):
"""
Run GATK RealignTargetCreator to find suspect intervals for realignment.
"""
input_bam0, input_bam1, input_bam2, input_bam3, input_bam4, input_bam5, input_bam6, input_bam7, input_bam8, input_bam9, input_bam10, input_bam11, input_bam12, input_bam13, input_bam14, input_bam15, input_bam16, input_bam17, input_bam18, input_bam19, input_bam20, input_bam21, input_bam22, input_bam23 = inputs
output_intervals, flag_file = outputs
logFile = mkLogFile(logDir, input_bam0, '.realignIntervals.log')
print "calculating realignment intervals for %s" % os.path.basename(input_bam0)
runStageCheck('realignIntervals', flag_file, ref_files['fasta_reference'], input_bam0, input_bam1, input_bam2, input_bam3, input_bam4, input_bam5, input_bam6, input_bam7, input_bam8, input_bam9, input_bam10, input_bam11, input_bam12, input_bam13, input_bam14, input_bam15, input_bam16, input_bam17, input_bam18, input_bam19, input_bam20, input_bam21, input_bam22, input_bam23, logFile, output_intervals)
def generate_normal_reads(ref_fasta, outputs):
fastq_r1, fastq_r2, flagFile = outputs
normal_out = '%s/%s' % (outdir, normal_outname)
cov = norm_cov + int(
(tumour_cov /
2)) #create normal component assuming half the "tumour" is normal
runStageCheck('generate_reads_simseq', flagFile, simseq_dir,
javasim_libdir, read_len, frag_len, frag_std, ref_fasta,
normal_reads, normal_out)
def callIndels(inputs, outputs):
"""
Use GATK UnifiedGenotyper to call indels from recalibrated bams.
"""
bam, _success = inputs
output_vcf, _idx, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.callIndels.log')
print "calling Indels from %s" % bam
runStageCheck('callIndels', flag_file, ref_files['fasta_reference'], bam,
ref_files['dbsnp'], logFile, output_vcf)
def filterIndels(inputs, outputs):
"""
Use GATK VariantFiltration to filter raw INDEL calls.
"""
input_vcf, _idx, _success = inputs
output_vcf, _idxout, flag_file = outputs
logFile = mkLogFile(logDir, input_vcf, '.filterIndels.log')
print "filtering indels from %s" % input_vcf
runStageCheck('filterIndels', flag_file, ref_files['fasta_reference'],
input_vcf, logFile, output_vcf)
def getEnsemblAnnotations(inputs, outputs):
"""
Annotate vcf using ENSEMBL variant effect predictor.
"""
vcf, _idx, _success = inputs
output, flag_file = outputs
logFile = mkLogFile(logDir, vcf, '.EnsemblAnnotation.log')
print "Annotating %s with ENSEMBL variant effect predictor" % os.path.basename(
vcf)
runStageCheck('annotateEnsembl', flag_file, vcf, output, logFile)
def collateReadCounts(inputs, outputs):
"""
Collate read counts from samtools flagstat output into a table.
"""
# Note expected input and output directories are effectively hard-coded
in_dir = sambam_dir
out_dir = results_dir
flag_file = outputs[-1]
print "Collating read counts"
runStageCheck('collateReadcounts', flag_file, in_dir, out_dir)
def mergeBams(inputs, outputs):
"""
Merge the sorted bams together for each sample.
Picard should cope correctly if there is only one input.
"""
bams = [bam for [bam, _success] in inputs]
output, flag_file = outputs
baminputs = ' '.join(["INPUT=%s" % bam for bam in bams])
print "merging %s into %s" % (",".join(
[os.path.basename(bam) for bam in bams]), os.path.basename(output))
runStageCheck('mergeBams', flag_file, baminputs, output)
def realignIntervals(inputs, outputs):
"""
Run GATK RealignTargetCreator to find suspect intervals for realignment.
"""
bam, _success = inputs
output_intervals, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.realignIntervals.log')
print "calculating realignment intervals for %s" % os.path.basename(bam)
runStageCheck('realignIntervals', flag_file, ref_files['fasta_reference'],
bam, ref_files['indels_realign_goldstandard'],
ref_files['indels_realign_1000G'], logFile, output_intervals)
def realign(inputs, outputs):
"""
Run GATK IndelRealigner for local realignment, using intervals found by realignIntervals.
"""
[intervals, _success], [input_bam] = inputs
output_bam, flag_file = outputs
logFile = mkLogFile(logDir, input_bam, '.realign.log')
print "realigning %s" % os.path.basename(input_bam)
runStageCheck('realign', flag_file, ref_files['fasta_reference'],
input_bam, intervals, logFile, output_bam)
remove_GATK_bai(output_bam)
def create_tumour_mixture(inputs, outputs):
fastq_r1, fastq_r2, _success = inputs
mix_r1, mix_r2, flagFile = outputs
match = re.search(r'(.*)\/([a-zA-Z0-9_\.]+)_R(1|2)\.fq', fastq_r1)
tumour_base = '%s/%s' % (match.group(1), match.group(2))
norm_base = '%s/%s' % (outdir, normal_outname)
mix_base = '%s/%s_mixture' % (match.group(1), match.group(2))
runStageCheck('create_tumour_mixture', flagFile, tumour_base, norm_base,
mix_base)
def finalDepthOfCoverage(inputs, outputs):
"""
Use GATK DepthOfCoverage to get coverage statistics.
"""
bam, _success = inputs
flag_file = outputs[-1]
output_example = outputs[0]
output_base = os.path.splitext(output_example)[0]
print "calculating coverage statistics using GATK DepthOfCoverage on %s" % bam
runStageCheck('depthOfCoverage', flag_file, ref_files['fasta_reference'],
bam, output_base)
def baseQualRecalCount(inputs, outputs):
"""
GATK CountCovariates, first step of base quality score recalibration.
"""
bam, _success = inputs
output_csv, flag_file = outputs
logFile = mkLogFile(logDir, bam, '.baseQualRecalCount.log')
print "count covariates using GATK for base quality score recalibration: %s" % os.path.basename(
bam)
runStageCheck('baseQualRecalCount', flag_file, bam,
ref_files['fasta_reference'], ref_files['dbsnp'], logFile,
output_csv)
def baseQualRecalTabulate(inputs, outputs):
"""
GATK TableRecalibration: recalibrate base quality scores using the output of CountCovariates.
"""
[input_csv, _success], [input_bam] = inputs
output_bam, flag_file = outputs
logFile = mkLogFile(logDir, input_bam, '.baseQualRecalTabulate.log')
print "recalibrate base quality scores using GATK on %s" % os.path.basename(
input_bam)
runStageCheck('baseQualRecalTabulate', flag_file, input_bam,
ref_files['fasta_reference'], input_csv, logFile, output_bam)
remove_GATK_bai(output_bam)
def align_tumour_reads(inputs, outputs):
fastq_r1, fastq_r2, _success = inputs
samFile, flagFile = outputs
outSam = '%s/%s.sam' % (outdir, tumour_outname)
if aligner == 'bowtie':
runStageCheck('align_tumour_reads_bowtie', flagFile, threads,
ref_fasta, fastq_r1, fastq_r2, outSam, tumour_outname,
tumour_outname)
elif aligner == 'bwa':
tumour_rg = '"@RG\\tID:%s\\t@SM:%s"' % (tumour_outname, tumour_outname)
runStageCheck('align_tumour_reads_bwa', flagFile, threads, ref_fasta,
fastq_r1, fastq_r2, tumour_rg, outSam)
else:
raise ValueError('Invalid aligner specified!')
def generate_tumour_reads(inputs, outputs):
variant_fasta, _success = inputs
fastq_r1, fastq_r2, flagFile = outputs
match = re.search('(.*)\/([a-zA-Z0-9_\.]+)\.fa_reference.fa',
variant_fasta)
tumour_out = '%s/%s' % (match.group(1), match.group(2))
cov = int(tumour_cov / 2) #assume variants occur only on one chromosome
# have to tweak tumour reads based on generated reference genome
proc = subprocess.Popen(["wc", variant_fasta], stdout=subprocess.PIPE)
wc_out = proc.stdout.readline().split()
tum_chrom_len = int(
wc_out[2]) - 4 #4 = number of characters in the fasta header
tumour_reads = (tum_chrom_len / frag_len) * int((tumour_cov / 2))
runStageCheck('generate_reads_simseq', flagFile, simseq_dir,
javasim_libdir, read_len, frag_len, frag_std, variant_fasta,
tumour_reads, tumour_out)
def bwaPE(inputs, outputs):
"""
Aligns two paired-end fastq files to a reference genome to produce a sam file.
"""
seq1, seq2 = sorted(inputs)
output, flag_file = outputs
fastq_name = os.path.basename(seq1)
sample = fastq_metadata[fastq_name]['sample']
runID = fastq_metadata[fastq_name]['run_id']
lane = fastq_metadata[fastq_name]['lane']
readgroup_metadata = {
'PL': 'ILLUMINA',
'SM': sample,
'ID': "%s_%s_Lane%d" % (sample, runID, lane)
}
metadata_str = make_metadata_string(readgroup_metadata)
print "bwa-mem on %s and %s" % (os.path.basename(seq1),
os.path.basename(seq2))
runStageCheck('bwaMemPE', flag_file, metadata_str,
ref_files['bwa_reference'], seq1, seq2, output)
def variants_to_bed(inputs, outputs):
variant_fasta, _success = inputs
variant_bed, flagFile = outputs
runStageCheck('variants_to_bed', flagFile, variant_fasta, variant_bed)