diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index a10eca543..a3463e62c 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -18,6 +18,7 @@ Added Changed ------- +- Remove ``rnaseqc-qc`` 3' bias statistics from MultiQC report Fixed ----- diff --git a/resolwe_bio/processes/support_processors/multiqc.py b/resolwe_bio/processes/support_processors/multiqc.py index 6b990a89f..0835c377a 100644 --- a/resolwe_bio/processes/support_processors/multiqc.py +++ b/resolwe_bio/processes/support_processors/multiqc.py @@ -64,43 +64,6 @@ def create_summary_table(samples, species, build): json.dump(sample_summary_json, out_file) -def parse_rnaseqc_report(report): - """Parse RNA-SeQC QC report file.""" - df = pd.read_csv(report, sep="\t") - return dict(df.values) - - -def create_coverage_table(sample_names, reports): - """Prepare coverage metrics table.""" - coverage_stats = [ - "Genes used in 3' bias", - "Mean 3' bias", - "Median 3' bias", - "3' bias Std", - "3' bias MAD_Std", - "3' Bias, 25th Percentile", - "3' Bias, 75th Percentile", - ] - - coverage_qc_json = { - "id": "coverage_qc", - "section_name": "RNA-SeQC Coverage Stats", - "plot_type": "table", - "file_format": "json", - "data": {}, - } - - for sample_name, report in zip(sample_names, reports): - report_data = parse_rnaseqc_report(report) - - coverage_qc_json["data"][sample_name] = { - k: report_data[k] for k in coverage_stats if k in report_data - } - - with open("rnaseqc_coverage_mqc.json", "w") as out_file: - json.dump(coverage_qc_json, out_file) - - def parse_chip_qc_report(report): """Parse ChiP-seq QC report file.""" df = pd.read_csv(report, sep="\t") @@ -439,7 +402,7 @@ class MultiQC(Process): } category = "QC" data_name = "MultiQC report" - version = "1.22.2" + version = "1.24.0" class Input: """Input fields to process MultiQC.""" @@ -517,8 +480,6 @@ def run(self, inputs, outputs): unsupported_data = [] star_quantification_samples = [] star_quantification_reports = [] - rnaseqc_samples = [] - rnaseqc_reports = [] config_file = "/opt/resolwebio/assets/multiqc_config.yml" with open(config_file) as handle: @@ -687,14 +648,9 @@ def run(self, inputs, outputs): elif d.process.type == "data:rnaseqc:qc:": name = os.path.basename(d.output.metrics.path) - rnaseqc_samples.append(sample_name) - rnaseqc_reports.append(d.output.metrics.path) create_symlink( src=d.output.metrics.path, dst=os.path.join(sample_dir, name) ) - create_coverage_table( - sample_names=rnaseqc_samples, reports=rnaseqc_reports - ) elif d.process.type == "data:expression:salmon:": # Symlink files/dirs without the parent directory to diff --git a/resolwe_bio/tests/processes/test_support_processors.py b/resolwe_bio/tests/processes/test_support_processors.py index 482ec22fd..5242e3b2c 100644 --- a/resolwe_bio/tests/processes/test_support_processors.py +++ b/resolwe_bio/tests/processes/test_support_processors.py @@ -491,14 +491,6 @@ def test_multiqc(self): }, ) - rnaseqc_report = self.run_process( - "rnaseqc-qc", - { - "alignment": star_alignment.id, - "annotation": annotation.id, - }, - ) - # BED file is not part of a sample entity. Test if MultiQC process # correctly skips this input data object bed = self.run_process( @@ -518,7 +510,6 @@ def test_multiqc(self): star_quantification.id, samtools_idxstats.id, qorts_report.id, - rnaseqc_report.id, bed.id, ], "advanced": {