def job_hisat2_align(
self = Default,
prefix = File,
INDEX_PREFIX = Prefix,
FASTQ_FILE_1 = InputFile,
FASTQ_FILE_2 = InputFile,
THREADS_ = int,
_IMAGE = "docker://quay.io/biocontainers/hisat2:2.1.0--py36hc9558a2_4",
_IMAGE_SAMTOOLS = "docker://quay.io/biocontainers/samtools:1.10--h9402c20_2",
_output = [
File('bam'),
File('log'),
File('cmd'),
]
):
# _out = get_output_files(self,prefix,_output)
results = []
CMD = [
'hisat2','-x',
Prefix(INDEX_PREFIX),
'-1', str( FASTQ_FILE_1),
'-2', str( FASTQ_FILE_2),
# '-U', InputFile( FASTQ_FILE_1),
# ['-2',InputFile( FASTQ_FILE_2) ] if FASTQ_FILE_2 else [],
'-S', str( self.output.bam +'.sam' ),
'--threads', str( THREADS_ ),
'--no-mixed',
'--rna-strandness','RF',
'--dta',
'--fr',
'&>', str( self.output.log),
]
CMD = list_flatten_strict(CMD)
res = SingularityShellCommand(CMD, _IMAGE, self.output.cmd)
# results.append(job_result( None, CMD, self.output))
_ = '''
samtools view /home/feng/temp/187R/187R-S1-2018_06_27_14:02:08/809_S1.sam -b --threads 4 -o 809_S1.bam
'''
CMD = [
'samtools','view',
File( self.output.bam+'.sam'),
'--threads',str(THREADS_),
'-o',
File( self.output.bam+'.unsorted'),
]
CMD = list_flatten_strict(CMD)
res = SingularityShellCommand(CMD, _IMAGE_SAMTOOLS, self.output.cmd)
CMD = [
'samtools','sort',
File( self.output.bam + '.unsorted'),
'--threads', str(THREADS_),
'-o',
File( self.output.bam),
]
CMD = list_flatten_strict(CMD)
res = SingularityShellCommand(CMD, _IMAGE_SAMTOOLS, self.output.cmd)
return self
def get_stringtie( BAM_FILE = Default, GTF_FILE = InputFile, THREADS = int, _IMAGE = 'docker://quay.io/biocontainers/stringtie:2.1.1--hc900ff6_0'): _= ''' stringtie -p 4 --rf 809_S1.bam -G /home/feng/ref/Arabidopsis_thaliana_TAIR10/annotation/genes.gtf -o 809_S1.stringtie.gtf -A 809_S1.stringtie.count &> 809_S1.stringtie.log ''' _out = _stringtie_output( COUNT_FILE = BAM_FILE + 'stringtie.count', ) CMD = [ 'stringtie', '-p', str(THREADS), InputFile(BAM_FILE), '--rf', '-G', InputFile(GTF_FILE), '-A', OutputFile(_out.COUNT_FILE), '&>', OutputFile(_out.COUNT_FILE + '.log'), ] CMD = list_flatten_strict(CMD) res = SingularityShellCommand(CMD, _IMAGE) return job_result( _out.COUNT_FILE, CMD, self.output)
def get_picard_dedup( self = Default, prefix = Prefix, BAM_FILE = InputFile, _IMAGE = 'docker://quay.io/biocontainers/picard:2.21.9--0', _output = ['bam'], ): _ =''' java -XX:ParallelGCThreads=4 -jar /home/feng/envs/pipeline_Bd/jar/MarkDuplicates.jar I=/home/feng/temp/187R/187R-S1-2018_06_27_14:02:08/809_S1.sorted.bam O=809_S1_dedup.bam M=809_S1.dupstat.log REMOVE_DUPLICATES=true ''' _out = _picard_dedup_output( BAM_FILE = OutputFile( rstrip( InputFile(BAM_FILE),'.bam') +'.dedup.bam'), ) PROG = 'singularity exec docker://quay.io/biocontainers/picard:2.21.9--0 picard'.split() CMD = [ 'picard', 'MarkDuplicates', # 'java','-XX:ParallelGCThreads=%s'%THREADS, 'I=%s'% InputFile( BAM_FILE ), 'O=%s'% OutputFile(_out.BAM_FILE ), 'M=%s'% OutputFile(_out.BAM_FILE +'.log') , ] CMD = list_flatten_strict(CMD) res = SingularityShellCommand(CMD, _IMAGE) return job_result( _out.BAM_FILE, CMD, self.output)
def job_trimmomatic(
self=Default,
prefix = File,
FASTQ_FILE_1 = InputFile,
FASTQ_FILE_2 = InputFile,
THREADS_ = int,
_IMAGE ='docker://quay.io/biocontainers/trimmomatic:0.35--6',
_output = [
File('fastq_1'),
File('fastq_2'),
File('log'),
File('cmd'),
],
):
_ = '''
trimmomatic PE -threads 4 -phred33
/home/feng/temp/187R/187R-S1-2018_06_27_14:02:08/809_S1_R1_raw.fastq
/home/feng/temp
/187R/187R-S1-2018_06_27_14:02:08/809_S1_R2_raw.fastq
809_S1_R1_raw_pass.fastq
809_S1_R1_raw_fail.fastq
809_S1_R2_raw_pass.fastq
809_S1_R2_raw_fail.fastq
ILLUMINACLIP:/home/Program_NGS_sl-pw-srv01/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa
:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15
'''
# _out = get_output_files(self, prefix, _output)
CMD = [
'trimmomatic','PE',
'-threads', str(THREADS_),
'-phred33',
File( FASTQ_FILE_1 ),
File( FASTQ_FILE_2 ),
File( self.output.fastq_1 ),
File( self.output.fastq_1 + '.fail'),
File( self.output.fastq_2 ),
File( self.output.fastq_2 + '.fail'),
'ILLUMINACLIP:'
'/usr/local/share/trimmomatic-0.35-6/adapters/TruSeq3-PE-2.fa'
':6:30:10',
'LEADING:3',
'TRAILING:3',
'MINLEN:36',
'SLIDINGWINDOW:4:15',
'&>',
File( self.output.log)
]
CMD = list_flatten_strict(CMD)
# res = SingularityShellCommand(CMD, )
res = SingularityShellCommand(CMD, _IMAGE, self.output.cmd)
return self