diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config index 73bffa1bf48c922a9a188af2e108ea5dc345d9ed..2c0f1c31a9c46b5f9f45699f3c1eb506d6c62e10 100644 --- a/workflow/conf/biohpc.config +++ b/workflow/conf/biohpc.config @@ -14,19 +14,19 @@ process { } withName: alignReads{ module = ['python/3.6.1-2-anaconda', 'bwa/intel/0.7.12', 'samtools/1.6'] - cpus = 32 + queue = '128GB,256GB,256GBv1' } withName: filterReads{ module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'sambamba/0.6.6', 'bedtools/2.26.0'] - cpus = 32 + queue = '128GB,256GB,256GBv1' } withName: experimentQC { module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1'] - cpus = 32 + queue = '128GB,256GB,256GBv1' } withName: convertReads { module = ['python/3.6.1-2-anaconda', 'samtools/1.6', 'bedtools/2.26.0'] - cpus = 32 + queue = '128GB,256GB,256GBv1' } withName: crossReads { module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2'] @@ -42,7 +42,7 @@ process { } withName: callPeaksMACS { module = ['python/3.6.1-2-anaconda', 'macs/2.1.0-20151222', 'phantompeakqualtools/1.2', 'UCSC_userApps/v317', 'bedtools/2.26.0'] - cpus = 32 + queue = '128GB,256GB,256GBv1' } withName: consensusPeaks { module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0'] diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py index 30ff74f037e994b8e939314983e964b98eb20c0b..e69813332281cc5a72983e35cbdc565cc2ded5d3 100644 --- a/workflow/tests/test_annotate_peaks.py +++ b/workflow/tests/test_annotate_peaks.py @@ -21,8 +21,8 @@ def test_annotate_peaks_singleend(): @pytest.mark.pairedend def test_annotate_peaks_pairedend(): - assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA..chipseeker_pie.pdf')) - assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA..chipseeker_upsetplot.pdf')) - annotation_file = test_output_path + 'ENCSR729LGA..chipseeker_annotation.csv' + assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_pie.pdf')) + assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf')) + annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.csv' assert os.path.exists(annotation_file) - assert utils.count_lines(annotation_file) == 25391 + assert utils.count_lines(annotation_file) == 25614 diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py index 99d43b87939617c801bad0389f14e2683cde0f82..36ed3da17e7eb61aa4440ae18527453d19a32df9 100644 --- a/workflow/tests/test_overlap_peaks.py +++ b/workflow/tests/test_overlap_peaks.py @@ -44,4 +44,4 @@ def test_overlap_peaks_singleend(): def test_overlap_peaks_pairedend(): assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak')) peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak' - assert utils.count_lines(peak_file) == 25655 + assert utils.count_lines(peak_file) == 25878