From 117ff7eed9609ad40529d8b3f827e19b186e04da Mon Sep 17 00:00:00 2001 From: Khurram Maqbool <5569347+khurrammaqbool@users.noreply.github.com> Date: Fri, 11 Oct 2024 12:52:16 +0200 Subject: [PATCH] feat: add msi tn to storage (#1483) * add MSI TN to storage * changelog * fix blank line * changelog --- BALSAMIC/constants/rules.py | 1 + BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule | 1 + CHANGELOG.rst | 3 ++- 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/BALSAMIC/constants/rules.py b/BALSAMIC/constants/rules.py index 4ef948b31..253a6c236 100644 --- a/BALSAMIC/constants/rules.py +++ b/BALSAMIC/constants/rules.py @@ -215,6 +215,7 @@ "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 4a06624f1..0cf8bd08e 100644 --- a/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule +++ b/BALSAMIC/snakemake_rules/annotation/msi_tumor_normal.rule @@ -41,6 +41,7 @@ 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 b05912b31..ffffbc396 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -5,7 +5,8 @@ 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 -* Sentieon install directory path to case config arguments https://github.com/Clinical-Genomics/BALSAMIC/pull/1461 +* Sentieon install directory path to case config arguments https://giithub.com/Clinical-Genomics/BALSAMIC/pull/1461 +* MSI tumor-normal analysis to housekeeper storage https://github.com/Clinical-Genomics/BALSAMIC/pull/1483 Changed: ^^^^^^^^