Commit 94118f99 authored by Gerald Salin's avatar Gerald Salin
Browse files

delete pngfiles as outputfileList

parent 70df192a
......@@ -50,12 +50,12 @@ class Bismark (Analysis):
if read2:
self.output_bam = OutputFileList(self.get_outputs('{basename}_bismark_bt2_pe.bam', read1), Formats.BAM)
self.output_report = OutputFileList(self.get_outputs('{basename}_bismark_bt2_PE_report.txt', read1))
self.output_alignment_overview_bam = OutputFileList(self.get_outputs('{basename}_bismark_PE.alignment_overview.png', read1))
#self.output_alignment_overview_bam = OutputFileList(self.get_outputs('{basename}_bismark_PE.alignment_overview.png', read1))
self.read2 = InputFileList(read2, Formats.FASTQ)
else :
self.output_bam = OutputFileList(self.get_outputs('{basename}_bismark_bt2.bam', read1), Formats.BAM)
self.output_report = OutputFileList(self.get_outputs('{basename}_bismark_bt2_SE_report.txt', read1))
self.output_alignment_overview_bam = OutputFileList(self.get_outputs('{basename}_bismark_SE.alignment_overview.png', read1))
#self.output_alignment_overview_bam = OutputFileList(self.get_outputs('{basename}_bismark_SE.alignment_overview.png', read1))
if non_directional :
self.args += " --non_directional"
......@@ -78,7 +78,7 @@ class Bismark (Analysis):
" " + self.reference_directory + " -1 $1 -2 $2 2> $5 ;" + \
self.get_exec_path("samtools") + " sort $3 $3 ;" + "mv $3.bam $4; " + \
self.get_exec_path("samtools") + " index $4; " + self.get_exec_path("samtools") +" calmd -b $4 "+self.reference_genome+" > $4.calmd 2>>$5; rm -f $4; mv $4.calmd $4 " , cmd_format='{EXE} {IN} {OUT}')
bismark_map = MultiMap(bismark_fn, inputs=[self.read1, self.read2], outputs=[self.output_bam,self.output_sorted_bam,self.stderrs,self.output_report,self.output_alignment_overview_bam], includes=self.reference_genome)
bismark_map = MultiMap(bismark_fn, inputs=[self.read1, self.read2], outputs=[self.output_bam,self.output_sorted_bam,self.stderrs,self.output_report], includes=self.reference_genome)
else:
# bismark_fn = ShellFunction(self.get_exec_path("bismark") + " " + self.args + " -o " + self.output_directory + \
# " " + self.reference_directory + " $1 2> $4 ;" + \
......@@ -92,7 +92,7 @@ class Bismark (Analysis):
" " + self.reference_directory + " $1 2> $4 ;" + \
self.get_exec_path("samtools") + " sort $2 $2 ;" + " mv $2.bam $3; " + \
self.get_exec_path("samtools") + " index $3; "+ self.get_exec_path("samtools") +" calmd -b $3 "+self.reference_genome+" > $3.calmd 2>>$4; rm -f $3; mv $3.calmd $3 " , cmd_format='{EXE} {IN} {OUT}')
bismark_map = MultiMap(bismark_fn, self.read1, outputs=[self.output_bam,self.output_sorted_bam,self.stderrs,self.output_report,self.output_alignment_overview_bam], includes=self.reference_genome)
bismark_map = MultiMap(bismark_fn, self.read1, outputs=[self.output_bam,self.output_sorted_bam,self.stderrs,self.output_report], includes=self.reference_genome)
def define_analysis(self):
self.name = "Alignment"
......@@ -111,7 +111,7 @@ class Bismark (Analysis):
# Finally create and add the archive to the analysis
self._save_files(self.output_sorted_bam)
self._save_files(self.output_report)
self._save_files(self.output_alignment_overview_bam)
#self._save_files(self.output_alignment_overview_bam)
def get_version(self):
cmd = [self.get_exec_path("bismark"),"--version"]
......
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