From cf00e0e580f6fff183be01f5a7cc52128091acc3 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 6 Jan 2019 19:30:21 -0600
Subject: [PATCH] Update file names and output for filter reads.
---
workflow/main.nf | 6 +++---
workflow/scripts/map_qc.py | 4 ++--
workflow/tests/test_map_qc.py | 18 ++++++++++--------
3 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 0f4b58f..3bd2edf 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -161,9 +161,9 @@ process filterReads {
set sampleId, file('*.bam'), file('*.bai'), experimentId, biosample, factor, treatment, replicate, controlId into dedupReads
set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into convertReads
- file '*flagstat.qc' into dedupReadsStats
- file '*pbc.qc' into dedupReadsComplexity
- file '*dup.qc' into dupReads
+ file '*.flagstat.qc' into dedupReadsStats
+ file '*.pbc.qc' into dedupReadsComplexity
+ file '*.dedup.qc' into dupReads
script:
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index 4cc549f..78b9298 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -169,7 +169,7 @@ def dedup_mapped(bam, bam_basename, paired):
# Remove duplicates
- final_bam_prefix = bam_basename + ".filt.nodup"
+ final_bam_prefix = bam_basename + ".dedup"
final_bam_filename = final_bam_prefix + ".bam"
if paired: # paired-end data
@@ -206,7 +206,7 @@ def dedup_mapped(bam, bam_basename, paired):
def compute_complexity(bam, paired, bam_basename):
'''Calculate library complexity .'''
- pbc_file_qc_filename = bam_basename + ".filt.nodup.pbc.qc"
+ pbc_file_qc_filename = bam_basename + ".pbc.qc"
tmp_pbc_file_qc_filename = "tmp.%s" % (pbc_file_qc_filename)
# Sort by name
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index 78e3b39..5ae8218 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -10,13 +10,14 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_map_qc_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam.bai'))
- filtered_reads_report = test_output_path + 'ENCFF646LXU.filt.nodup.flagstat.qc'
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.dedup.bam'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.dedup.bam.bai'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI.dedup.qc'))
+ filtered_reads_report = test_output_path + 'ENCLB831RUI.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines()
assert '64962570 + 0 in total' in samtools_report[0]
assert '64962570 + 0 mapped (100.00%:N/A)' in samtools_report[4]
- library_complexity = test_output_path + 'ENCFF646LXU.filt.nodup.pbc.qc'
+ library_complexity = test_output_path + 'ENCLB831RUI.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.926192
assert df_library_complexity["PBC1"].iloc[0] == 0.926775
@@ -25,13 +26,14 @@ def test_map_qc_singleend():
@pytest.mark.pairedend
def test_map_qc_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bam'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bambai'))
- filtered_reads_report = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.flagstat.qc'
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.dedup.bam'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.dedup.bam.bai'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.dedup.qc'))
+ filtered_reads_report = test_output_path + 'ENCLB568IYX.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines()
assert '47389080 + 0 in total' in samtools_report[0]
assert '47389080 + 0 mapped (100.00%:N/A)' in samtools_report[4]
- library_complexity = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.pbc.qc'
+ library_complexity = test_output_path + 'ENCLB568IYX.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.947064
assert df_library_complexity["PBC1"].iloc[0] == 0.946724
--
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