Commit c4be5af4 authored by Penom Nom's avatar Penom Nom
Browse files

Add option to delete bams.

parent 53a98dca
......@@ -107,7 +107,7 @@ class CasavaQualityCheck (NG6Workflow):
sample_lane_prefixes = None
if group_prefix is not None :
sample_lane_prefixes = (Utils.get_group_basenames(filtered_read1_files+filtered_read2_files, "lane")).keys()
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes], parent = fastqilluminafilter)
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "aln", not self.args["delete_bam"]], parent = fastqilluminafilter)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [bwa.bam_files, is_paired_end, False], parent = bwa)
......
......@@ -72,6 +72,11 @@ keep_reads.help = Keep reads which pass the Illumina filters or keep reads which
keep_reads.default = pass_illumina_filters
keep_reads.choices = pass_illumina_filters|not_pass_illumina_filters|all
delete_bam = delete_bam
delete_bam.flag = --delete-bam
delete_bam.help = The BAM are not stored.
delete_bam.default = False
histogram_width.name = histogram_width
histogram_width.flag = --histogram_width
histogram_width.help = Explicitly sets the histogram width, overriding automatic truncation of histogram tail.
......
......@@ -31,7 +31,7 @@ from weaver.abstraction import Map
class BWA (Analysis):
def define_parameters(self, reference_genome, read1, read2=None, group_prefix=None, algorithm="aln"):
def define_parameters(self, reference_genome, read1, read2=None, group_prefix=None, algorithm="aln", keep_bam=True):
self.read1 = InputFileList(read1, Formats.FASTQ)
self.read2=None
if algorithm=="aln":
......@@ -55,6 +55,7 @@ class BWA (Analysis):
self.group_prefix = group_prefix
self.algorithm = algorithm
self.keep_bam = keep_bam
self.reference_genome = InputFile(reference_genome)
#################################PATCH############################################
self.source_file = reference_genome + "_source"
......@@ -75,8 +76,9 @@ class BWA (Analysis):
##################################################################################
def post_process(self):
# Finally create and add the archive to the analysis
self._save_files(self.bam_files)
if self.keep_bam:
# Finally create and add the archive to the analysis
self._save_files(self.bam_files)
def get_version(self):
cmd = [self.get_exec_path("bwa")]
......
......@@ -107,7 +107,7 @@ class IlluminaQualityCheck (NG6Workflow):
sample_lane_prefixes = None
if group_prefix is not None :
sample_lane_prefixes = (Utils.get_group_basenames(filtered_read1_files+filtered_read2_files, "lane")).keys()
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes], parent = fastqilluminafilter)
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "aln", not self.args["delete_bam"]], parent = fastqilluminafilter)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [bwa.bam_files, is_paired_end, True], parent = bwa)
......
......@@ -72,6 +72,11 @@ keep_reads.help = Keep reads which pass the Illumina filters or keep reads which
keep_reads.default = pass_illumina_filters
keep_reads.choices = pass_illumina_filters|not_pass_illumina_filters|all
delete_bam = delete_bam
delete_bam.flag = --delete-bam
delete_bam.help = The BAM are not stored.
delete_bam.default = False
histogram_width.name = histogram_width
histogram_width.flag = --histogram_width
histogram_width.help = Explicitly sets the histogram width, overriding automatic truncation of histogram tail.
......
......@@ -105,7 +105,7 @@ class RnaSeqQualityCheck (NG6Workflow):
sample_lane_prefixes = None
if group_prefix is not None :
sample_lane_prefixes = (Utils.get_group_basenames(filtered_read1_files+filtered_read2_files, "lane")).keys()
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes], parent = fastqilluminafilter)
bwa = self.add_component("BWA", [indexed_ref, filtered_read1_files, filtered_read2_files, sample_lane_prefixes, "aln", not self.args["delete_bam"]], parent = fastqilluminafilter)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [bwa.bam_files, is_paired_end], parent = bwa, component_prefix="bwa")
......@@ -129,7 +129,7 @@ class RnaSeqQualityCheck (NG6Workflow):
concat_read2_files = filtered_read2_files
concat_read1_files = sorted(concat_read1_files)
concat_read2_files = sorted(concat_read2_files)
tophat = self.add_component("TopHat", [indexed_ref, concat_read1_files, concat_read2_files], parent = fastqilluminafilter)
tophat = self.add_component("TopHat", [indexed_ref, concat_read1_files, concat_read2_files, "25000", "6", not self.args["delete_bam"]], parent = fastqilluminafilter)
# make some statistic on the alignement
alignmentstats = self.add_component("AlignmentStats", [tophat.bam_files, is_paired_end], parent = tophat, component_prefix="tophat")
......
......@@ -32,7 +32,7 @@ from ng6.utils import Utils
class TopHat (Analysis):
def define_parameters(self, index_ref_genome, read1, read2, max_intron_length="25000", nb_threads="6", archive_name=None):
def define_parameters(self, index_ref_genome, read1, read2, max_intron_length="25000", nb_threads="6", keep_bam=True, archive_name=None):
self.read1 = InputFileList(read1, Formats.FASTQ)
self.read2 = None
......@@ -55,6 +55,7 @@ class TopHat (Analysis):
self.max_intron_length = max_intron_length
self.nb_threads = nb_threads
self.keep_bam = keep_bam
def define_analysis(self):
self.name = "TopHat Alignment"
......@@ -63,8 +64,9 @@ class TopHat (Analysis):
self.options = self.max_intron_length + " " + self.nb_threads
def post_process(self):
# Finally create and add the archive to the analysis
self._save_files(self.bam_files)
if self.keep_bam:
# Finally create and add the archive to the analysis
self._save_files(self.bam_files)
def get_version(self):
cmd = [self.get_exec_path("tophat2"), "-v"]
......
......@@ -55,6 +55,11 @@ keep_reads.help = Keep reads which pass the Illumina filters or keep reads which
keep_reads.default = pass_illumina_filters
keep_reads.choices = pass_illumina_filters|not_pass_illumina_filters|all
delete_bam = delete_bam
delete_bam.flag = --delete-bam
delete_bam.help = The BAM are not stored.
delete_bam.default = False
compression.name = compression
compression.flag = --compression
compression.help = How should data be compressed once archived (none|gz|bz2)
......
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