From 556fc8c183805b086008043a9c3cf13ced48e767 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 28 Jul 2014 15:49:40 +0200
Subject: [PATCH] Output cutadapt statistics correctly in summary files
---
.../pipelines/flexiprep/scripts/summarize_flexiprep.py | 7 +++++--
.../lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 3 +++
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
index cdf952472..d322c3c83 100755
--- a/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
+++ b/flexiprep/scripts/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/summarize_flexiprep.py
@@ -91,7 +91,7 @@ def clip2dict(sample, samplea, sampleb, lib_type, run_dir):
def get_cutadapt_stats(read_pair, adapter_dict):
stats = {}
- stat_file = read_pair + '.clipstat'
+ stat_file = read_pair + '.clip.stats'
try:
with open_result(stat_file) as src:
@@ -152,7 +152,10 @@ def sickle2dict(run_name, qc_mode, lib_type, run_dir):
if qc_mode == 'trim':
stat_mark = '.trim.stats'
else:
- stat_mark = '.clip.sync.trim.stats'
+ if lib_type == 'paired':
+ stat_mark = '.clip.sync.trim.stats'
+ else:
+ stat_mark = '.clip.trim.stats'
if lib_type == 'paired':
re_paired_kept = re.compile(r'paired records kept: \d+ \((\d+) pairs\)')
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index f2fc812ee..0bb1fd9ee 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -137,6 +137,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
cutadapt_R1.fastq_input = R1
cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip" + R1_ext)
cutadapt_R1.stats_output = swapExt(outDir, R1, R1_ext, ".clip.stats")
+ outputFiles += ("cutadapt_R1_stats" -> cutadapt_R1.stats_output)
if (outputFiles.contains("contams_R1")) cutadapt_R1.contams_file = outputFiles("contams_R1")
@@ -148,6 +149,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
if (!skipTrim || paired) cutadapt_R2.isIntermediate = true
cutadapt_R2.fastq_input = R2
cutadapt_R2.fastq_output = swapExt(outDir, R2, R2_ext, ".clip" + R2_ext)
+ cutadapt_R2.stats_output = swapExt(outDir, R2, R2_ext, ".clip.stats")
+ outputFiles += ("cutadapt_R2_stats" -> cutadapt_R2.stats_output)
if (outputFiles.contains("contams_R2")) cutadapt_R2.contams_file = outputFiles("contams_R2")
add(cutadapt_R2)
R2 = cutadapt_R2.fastq_output
--
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