From 385740c8a7ef0d754784d8f2480cc0d259db9311 Mon Sep 17 00:00:00 2001 From: ashwini06 Date: Mon, 4 Apr 2022 14:18:27 +0200 Subject: [PATCH 1/2] docs: fix version and doc text (#888) * fix the right version in install docs * add umi pre-call text to balsamic filters doc --- .bumpversion.cfg | 3 +++ CHANGELOG.rst | 13 +++++++++++++ docs/balsamic_filters.rst | 28 +++++++++++++++++++++++++--- docs/install.rst | 2 +- 4 files changed, 42 insertions(+), 4 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 7b4884c63..45b4d83c9 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -17,6 +17,9 @@ tag_name = v{new_version} [bumpversion:file:docs/bioinfo_softwares.rst] [bumpversion:file:docs/user_guide.rst] + +[bumpversion:file:docs/install.rst] + search = {current_version} replace = {new_version} diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 6ae655c29..e31036fcc 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,19 @@ +[8.2.9] +------- + + + [8.2.8] ------- +Added: +^^^^^^ +* Included more text about UMI-workflow variant calling settings to the readthedocs + +Fixes: +^^^^^^ +* Automate balsamic version for readthedocs install page + Added: ^^^^^^ * Added the readthedocs page for BALSAMIC variant-calling filters #867 diff --git a/docs/balsamic_filters.rst b/docs/balsamic_filters.rst index 80e2b0361..ac774b2c0 100644 --- a/docs/balsamic_filters.rst +++ b/docs/balsamic_filters.rst @@ -33,7 +33,6 @@ indicate that at this site, the mean position in reads is less than 8 and positi For `Post-call filtering`, in BALSAMIC we have applied various filtering criteria (`Vardict_filtering`_, `TNscope filtering (Tumor_normal)`_ ) depending on the analysis-type (TGS/WGS) and sample-type(tumor-only/tumor-normal). .. important:: - In BALSAMIC, this VCF file is named as `*.all.filtered.pass.vcf.gz` (eg: `SNV.somatic..vardict.all.filtered.pass.vcf.gz`) **Targeted Genome Analysis** @@ -80,7 +79,6 @@ Following are the set of criterias applied for filtering vardict results. Applie Maximum AF < 1 .. attention:: - BALSAMIC <= v8.2.7 uses minimum AF 1% (0.01). From Balsamic v8.2.8, minimum VAF is changed to 0.7% (0.007) *GNOMADAF_POPMAX*: Maximum Allele Frequency across populations @@ -90,7 +88,6 @@ Following are the set of criterias applied for filtering vardict results. Applie GNOMADAF_popmax <= 0.005 (or) GNOMADAF_popmax == "." .. important:: - Additionally, for tumor-normal cases; the variant is excluded if it marked as 'germline' in the `STATUS` column of vcf file. **Whole Genome Sequencing (WGS)** @@ -187,6 +184,31 @@ The `TNscope `_ algor `UMI workflow `_ performs the variant calling of SNVs/INDELS using the `TNscope` algorithm from UMI consensus-called reads. The following filter applies for both tumor-normal and tumor-only samples. +**Pre-call Filters** + +*minreads*: Filtering of consensus called reads based on the minimum reads supporting each UMI tag group + +:: + + minreads = 3,1,1 + +Which means that at least `3` UMI tag groups should be ideally considered from both DNA strands, where a minimum of atleast `1` UMI tag group should exist in each of the single-stranded consensus reads. + +*min_init_tumor_lod* : Log odds is the likelihood that the candidate mutation is real over the likelihood that the candidate mutation is a sequencing error before any read-based filters are applied. +minimum log odds for the candidate selection. TNscope default: `4` + +:: + + min_init_tumor_lod = 0.5 + +*min_tumor_lod* : minimum log odds in the final call of variants. TNscope default: `6.3` + +:: + + min_tumor_lod = 4.0 + +**Post-call Filters** + *GNOMADAF_POPMAX*: Maximum Allele Frequency across populations :: diff --git a/docs/install.rst b/docs/install.rst index 5971c5afa..4e67c4eb9 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -2,7 +2,7 @@ Installation ============ -This section describes steps to install BALSAMIC (**version** = 4.1.0) +This section describes steps to install BALSAMIC (**version** = 8.2.8) From 9578e977d9308762a1fcafb88931b3537a25f548 Mon Sep 17 00:00:00 2001 From: ashwini06 Date: Mon, 4 Apr 2022 16:11:48 +0200 Subject: [PATCH 2/2] fix: qos express (#887) * add new QoS tag to `express` balsamic cli --- .github/workflows/black_linter.yml | 2 +- BALSAMIC/commands/init/base.py | 2 +- BALSAMIC/commands/run/analysis.py | 2 +- CHANGELOG.rst | 17 ++++++++++++++++- requirements-dev.txt | 2 +- 5 files changed, 20 insertions(+), 5 deletions(-) diff --git a/.github/workflows/black_linter.yml b/.github/workflows/black_linter.yml index 9686afda6..5e9cad8b6 100644 --- a/.github/workflows/black_linter.yml +++ b/.github/workflows/black_linter.yml @@ -11,4 +11,4 @@ jobs: - uses: psf/black@stable with: options: "--check --verbose" - version: "21.7b0" + version: "22.3.0" diff --git a/BALSAMIC/commands/init/base.py b/BALSAMIC/commands/init/base.py index 8c33252ca..6adfc5d10 100644 --- a/BALSAMIC/commands/init/base.py +++ b/BALSAMIC/commands/init/base.py @@ -126,7 +126,7 @@ ) @click.option( "--qos", - type=click.Choice(["low", "normal", "high"]), + type=click.Choice(["low", "normal", "high", "express"]), show_default=True, default="low", help="QOS for sbatch jobs. Passed to " + get_schedulerpy(), diff --git a/BALSAMIC/commands/run/analysis.py b/BALSAMIC/commands/run/analysis.py index 87dfb156d..2bd4896a8 100644 --- a/BALSAMIC/commands/run/analysis.py +++ b/BALSAMIC/commands/run/analysis.py @@ -106,7 +106,7 @@ ) @click.option( "--qos", - type=click.Choice(["low", "normal", "high"]), + type=click.Choice(["low", "normal", "high", "express"]), show_default=True, default="low", help="QOS for sbatch jobs. Passed to " + get_schedulerpy(), diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e31036fcc..b27a80a39 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,7 +1,22 @@ -[8.2.9] +[X.X.X] ------- +Added: +^^^^^^ +* Added slurm qos tag `express` #885 +* Included more text about UMI-workflow variant calling settings to the readthedocs #888 + + +Fixes: +^^^^^^ +* Automate balsamic version for readthedocs install page #888 + +Changed: +^^^^^^^^ +Upgrade black to 22.3.0 + + [8.2.8] ------- diff --git a/requirements-dev.txt b/requirements-dev.txt index 0a65f8f27..c2fedd5f7 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,6 +2,6 @@ pytest>=3.7.1 pytest-cov==2.8.1 coveralls pylint -black==21.7b0 +black==22.3.0 pillow>=8.4.0 fpdf2>=2.4.6