Commit b60303e6 authored by Audrey Gibert's avatar Audrey Gibert
Browse files

RNAseq analysis has been commented because of a workflow bug #30

parent 9596d46c
......@@ -89,5 +89,7 @@ class RnaSeqQualityCheck (CasavaNG6Workflow):
alignmentstats = self.add_component("AlignmentStats", [star.output_bams, self.is_paired_end()], parent = star, component_prefix="star")
#Quality RNA Seq analysis
if self.annotation:
rseqc = self.add_component("RSeQC", [star.output_bams, self.annotation], parent = star)
# 02/08/2018 Audrey Gibert (était-ce un boulet?)
# C'est commenté parce qu'on a un bug à cause du script inner_distance.py "start must be smaller than end..." c'est embetant, on ne s'en sert jamais voilà voilà
# if self.annotation:
# rseqc = self.add_component("RSeQC", [star.output_bams, self.annotation], parent = star)
......@@ -76,7 +76,7 @@ class STAR (Analysis):
# sort
self.add_shell_execution( self.get_exec_path("samtools") + ' view -Sb $1 | ' + self.get_exec_path("samtools") +
' sort -@ ' + str(self.n_threads) + ' -f - -o $2 ' , cmd_format='{EXE} {IN} {OUT}', map=True,
' sort -@ ' + str(self.n_threads) + ' - -o $2 ' , cmd_format='{EXE} {IN} {OUT}', map=True,
inputs = [self.output_sams_no_md], outputs = [self.output_sorted_bams])
#calmd and convert to bam
......
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