diff --git a/workflow/.DS_Store b/workflow/.DS_Store index 1cfdf47763f95697736ca7303755f243846e9ca2..a563988c14d65d2b69eb3b32e875d0f346a3055a 100644 Binary files a/workflow/.DS_Store and b/workflow/.DS_Store differ diff --git a/workflow/scripts/experiment_qc.py b/workflow/scripts/experiment_qc.py index affbbc4946327810a366c59b44c58469466d91a4..34bce3a1516895044d32a9e8853b670b03255361 100644 --- a/workflow/scripts/experiment_qc.py +++ b/workflow/scripts/experiment_qc.py @@ -119,7 +119,7 @@ def check_coverage(design, extension): bam_files = ' '.join(design['bam_reads']) labels = ' '.join(design['sample_id']) - coverage_filename = 'coverage.png' + coverage_filename = 'coverage.pdf' coverage_params = "-n 1000000 --plotTitle \"Sample Coverage\"" + \ " --ignoreDuplicates --minMappingQuality 10" @@ -155,7 +155,7 @@ def update_controls(design): def check_enrichment(sample_id, control_id, sample_reads, control_reads, extension): '''Asses the enrichment per sample.''' - fingerprint_filename = sample_id + '_fingerprint.png' + fingerprint_filename = sample_id + '_fingerprint.pdf' fingerprint_command = ( "plotFingerprint -b %s %s --extendReads %d --labels %s %s --plotFile %s"