diff --git a/workflow/main.nf b/workflow/main.nf index 3bd2edf01fc2191bdfe863e785cc4821128350b9..ac29389dc993ebfd8e2034712d4cbf24168fdb2a 100644 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -342,6 +342,7 @@ process callPeaksMACS { output: set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks + file '*.xls' into summit script: diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py index 23174e07936ec09ccf494d1c713bd71bb4d72713..28c546c5c606c9a534a80de2f363a4e7adb52adf 100644 --- a/workflow/scripts/call_peaks_macs.py +++ b/workflow/scripts/call_peaks_macs.py @@ -125,7 +125,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes) # MACS2 sometimes calls features off the end of chromosomes. # Remove coordinates outside chromosome sizes - narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix) + narrowpeak_fn = '%s.narrowPeak' % (prefix) clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn) diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py index 71358bc045801d23d28b8f7385c5ef9f608347b6..dabfd7167f1e295735066db378028d17124e2654 100644 --- a/workflow/tests/test_call_peaks_macs.py +++ b/workflow/tests/test_call_peaks_macs.py @@ -12,7 +12,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ def test_call_peaks_macs_singleend(): assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw')) - peak_file = test_output_path + 'ENCLB144FDT_peaks.narrowPeak' + assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.xls')) + peak_file = test_output_path + 'ENCLB144FDT.narrowPeak' assert utils.count_lines(peak_file) == 227389 @@ -20,5 +21,6 @@ def test_call_peaks_macs_singleend(): def test_call_peaks_macs_pairedend(): assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.fc_signal.bw')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw')) - peak_file = test_output_path + 'ENCLB568IYX_peaks.narrowPeak' + assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.xls')) + peak_file = test_output_path + 'ENCLB568IYX.narrowPeak' assert utils.count_lines(peak_file) == 112652