diff --git a/BALSAMIC/constants/rules.py b/BALSAMIC/constants/rules.py index 1e9fc1e49..ff25ca37f 100644 --- a/BALSAMIC/constants/rules.py +++ b/BALSAMIC/constants/rules.py @@ -229,6 +229,7 @@ "finalize_gens_outputfiles", # TMB "tmb_calculation", + "msisensorpro_msi_tumor_normal", # CNV report "merge_cnv_pdf_reports", ] diff --git a/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule b/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule index b2291a246..167b188a6 100644 --- a/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule +++ b/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule @@ -42,6 +42,7 @@ rule msisensorpro_msi_tumor_normal: params: tmpdir=tempfile.mkdtemp(prefix=tmp_dir), case_id=config["analysis"]["case_id"], + housekeeper_id={"id": config["analysis"]["case_id"],"tags": "research"}, message: "Analysing MSI using msisensor-pro for {params.case_id}" shell: diff --git a/CHANGELOG.rst b/CHANGELOG.rst index d07b58c82..db224a89f 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -5,12 +5,14 @@ Added: ^^^^^^ * MSIsensor-pro container https://github.com/Clinical-Genomics/BALSAMIC/pull/1444 * MSI analysis to the tumor-normal workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1454 +* MSI tumor-normal analysis to housekeeper storage https://github.com/Clinical-Genomics/BALSAMIC/pull/1483 * Sentieon install directory path to case config arguments https://github.com/Clinical-Genomics/BALSAMIC/pull/1461 * UMI extraction and deduplication to TGA workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1358 * GENS input files for TGA https://github.com/Clinical-Genomics/BALSAMIC/pull/1448 * Padding of bed-regions for CNVkit to minimum 100 bases https://github.com/Clinical-Genomics/BALSAMIC/pull/1469 * Added min mapq 20 to CNVkit PON workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1465 * CNVkit PONs for Exome comprehensive 10.2, GMSsolid 15.2, GMCKsolid 4.2 https://github.com/Clinical-Genomics/BALSAMIC/pull/1465 +* Sentieon install directory path to case config arguments https://giithub.com/Clinical-Genomics/BALSAMIC/pull/1461 Changed: ^^^^^^^^