fix: command in vcf2cytosure rule and update ReadtheDocs

BALSAMIC/snakemake_rules/annotation/vcf2cytosure_convert.rule

@@ -70,7 +70,7 @@ elif config["analysis"]["sequencing_type"] == "wgs" and config["analysis"]["anal
         message: "Converting CNVs from VCF to the CGH format using vcf2cytosure for {params.case_name}"
         shell:
             """
-grep -E "#|PASS" {input.ascat_vcf} | bgzip -l 9 -c > {output.ascat_vcf};
+zgrep -E "#|PASS" {input.ascat_vcf} | bgzip -l 9 -c > {output.ascat_vcf};
 
 vcf2cytosure --vcf {output.ascat_vcf} --coverage {input.tiddit_cov_tumor} --out {output.cgh_tumor} --sex {params.gender} --bins 20
 

BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_normal.rule

@@ -22,7 +22,7 @@ rule manta_tumor_normal:
         tumor = get_sample_type(config["samples"], "tumor"),
         normal = get_sample_type(config["samples"], "normal"),
         case_name = config["analysis"]["case_id"],
-        manta_install_path = "/opt/conda/share/manta-1.6.0-1"
+        manta_install_path = "/opt/conda/share/manta-1.6.0-2"
     threads:
         get_threads(cluster_config, "manta_tumor_normal")
     message:

BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule

@@ -19,7 +19,7 @@ rule manta_tumor_only:
         runmode = "local",
         tumor = get_sample_type(config["samples"], "tumor"),
         case_name = config["analysis"]["case_id"],
-        manta_install_path= "/opt/conda/share/manta-1.6.0-1"
+        manta_install_path= "/opt/conda/share/manta-1.6.0-2"
     threads:
         get_threads(cluster_config, "manta_tumor_only")
     message:

CHANGELOG.rst

@@ -37,6 +37,7 @@ Fixed:
 * `run_validate.sh` script https://github.com/Clinical-Genomics/BALSAMIC/pull/952
 * Somatic SV tumor normal rules https://github.com/Clinical-Genomics/BALSAMIC/pull/959
 * Missing `genderChr` flag for `ascat_tumor_normal` rule https://github.com/Clinical-Genomics/BALSAMIC/pull/963
+* Command in vcf2cytosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966
 
 Removed
 ^^^^^^^

docs/FAQs.rst

@@ -96,59 +96,3 @@ Make a pull request to master at this point. After pull request is approved and
 - Never force rebase commits into either `master` or `develop` branches.
 - When merging pull requests commits into `master` branch, use **Create a merge commit**, which helps to capture all the commit history. On contrary, when merging pull requests into `develop` branch, use **Squash and merge** button, which combines multiple commits messages into one commit.
 
-**References**
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-**How to generate reference files for ascatNGS**
-
-Detailed information is available from `ascatNGS <https://github.com/cancerit/ascatNgs>`_ documentation
-
-Briefly, ascatNGS needs gender loci file if gender information for the input sample is not available. The second file is *SnpGcCorrections.tsv*, which is prepared from the 1000 genome SNP panel.
-
-1. **Gender loci file:**
-
-GRCh37d5_Y.loci contains the following contents:
-
-.. line-block::
-    Y	4546684
-    Y	2934912
-    Y	4550107
-    Y	4549638
-
-
-2. **GC correction file:**
-
-First step is to download the 1000 genome snp file and convert it from .vcf to .tsv. The detailed procedure to for this step is available from `ascatNGS-reference-files <https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs>`_ (Human reference files from 1000 genomes VCFs)
-
-.. code-block::
-
-    export TG_DATA=ftp://ftp.ensembl.org/pub/grch37/release-83/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz
-
-
-Followed by:
-
-.. code-block::
-
-    curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\
-    perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/);\
-    next if($F[0] eq $l_c && $F[1]-1000 < $l_p); $F[7]=~m/MAF=([^;]+)/;\
-    next if($1 < 0.05); printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1];\
-    $l_c=$F[0]; $l_p=$F[1];' > SnpPositions_GRCh37_1000g.tsv
-
-
---or--
-
-.. code-block::
-
-    curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\
-    perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/); $F[7]=~m/MAF=([^;]+)/;\
-    next if($1 < 0.05); next if($F[0] eq $l_c && $F[1]-1000 < $l_p);\
-    printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1]; $l_c=$F[0]; $l_p=$F[1];'\
-    > SnpPositions_GRCh37_1000g.tsv
-
-Second step is to use *SnpPositions.tsv* file and generate *SnpGcCorrections.tsv* file, more details see `ascatNGS-convert-snppositions <https://github.com/cancerit/ascatNgs/wiki/Convert-SnpPositions.tsv-to-SnpGcCorrections.tsv>`_
-
-.. code-block::
-
-    ascatSnpPanelGcCorrections.pl genome.fa SnpPositions.tsv > SnpGcCorrections.tsv
-

docs/README.rst

@@ -1,5 +1,5 @@
 =========
-Build Doc
+Build doc
 =========
 
 Following steps explains how to build documents locally.

docs/balsamic_annotation.rst

@@ -1,5 +1,5 @@
 ***********************************
-Annotation Resources
+Annotation resources
 ***********************************
 
 BALSAMIC annotates somatic single nucleotide variants (SNVs) using ``ensembl-vep`` and ``vcfanno``. Somatic structural variants (SVs), somatic copy-number variants (CNVs) and germline single nucleotide variants are annotated using only ``ensembl-vep``. All SVs and CNVs are merged using ``SVDB`` before annotating for `Target Genome Analysis (TGA)` or `Whole Genome Sequencing (WGS)` analyses.

docs/balsamic_filters.rst

@@ -1,9 +1,52 @@
 ***********************************
-Calling and Filtering Variants
+Calling and filtering variants
 ***********************************
 
-In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants. Also, the choice of these tools differs between the type of analysis,
-e.g.: `Target Genome Analysis (TGA)` or analysis of `Whole Genome Sequencing (WGS)`. Various filters (Pre-call and Post-call filtering) are applied at different levels to report high-confidence variant calls.
+In BALSAMIC, various bioinfo tools are integrated for reporting somatic and germline variants summarized in the table below. The choice of these tools differs between the type of analysis, `Target Genome Analysis (TGA)` or analysis of `Whole Genome Sequencing (WGS)`.
+
+
+.. list-table:: SNV and small-Indel callers
+   :widths: 22 27 25 20 20
+   :header-rows: 1
+
+   * - Variant caller
+     - Sequencing type
+     - Analysis type
+     - Somatic/Germline
+     - Variant type
+   * - DNAscope
+     - WGS
+     - tumor-normal, tumor-only
+     - germline
+     - SNV, InDel
+   * - TNhaplotyper
+     - TGA, WES, WGS :superscript:`1`
+     - tumor-normal, tumor-only
+     - somatic
+     - SNV, InDel
+   * - TNscope :superscript:`2`
+     - WGS
+     - tumor-normal, tumor-only
+     - somatic
+     - SNV, InDel
+   * - TNScope_umi
+     - TGA, WGS
+     - tumor-normal, tumor-only
+     - somatic, germline
+     - SNV, InDel
+   * - VarDict
+     - TGA, WGS
+     - tumor-normal, tumor-only
+     - somatic
+     - SNV, InDel
+
+:superscript:`1` TNhaplotyper is only executed for tumor-only if a WGS case is being analysed
+
+:superscript:`2` TNscope output is being merged with TNhaplotyper calls for TO-WGS analysis
+
+
+
+Various filters (Pre-call and Post-call filtering) are applied at different levels to report high-confidence variant calls.
 
 **Pre-call filtering** is where the variant-calling tool decides not to add a variant to the VCF file if the default filters of the variant-caller did not pass the filter criteria. The set of default filters differs between the various variant-calling algorithms.
 

docs/balsamic_methods.rst

@@ -1,6 +1,6 @@
-========
-Methods
-========
+===================
+Method description
+===================
 
 Target Genome Analysis
 ~~~~~~~~~~~~~~~~~~~~~~

docs/balsamic_sv_cnv.rst

@@ -1,5 +1,5 @@
 ************************************
-Structural and Copy Number Variants
+Structural and Copy Number variants
 ************************************
 
 Depending on the sequencing type, BALSAMIC is currently running the following structural and copy number variant callers:
@@ -42,6 +42,8 @@ Depending on the sequencing type, BALSAMIC is currently running the following st
 
 Further details about a specific caller can be found in the links for the repositories containing the documentation for SV and CNV callers along with the links for the articles are listed in `bioinfo softwares <https://github.com/Clinical-Genomics/BALSAMIC/blob/master/docs/bioinfo_softwares.rst>`_.
 
+It mandatory to provide the gender of the sample from BALSAMIC version >= 10.0.0 For CNV analysis.
+
 The copy number variants, identified using ascatNgs and `dellycnv`, are converted to deletion and duplications before they are merged using `SVDB` with `--bnd_distance = 5000` (distance between end points for the variants from different callers) and  `--overlap = 0.80` (percentage for overlapping bases for the variants from different callers). `SVDB` prioritizes the merging of variants from SV and CNV callers to fetch position and genotype information,  in the following order:
 
 .. list-table:: SVDB merge caller priority order
@@ -81,4 +83,52 @@ The following command can be used to fetch the variants identified by a specific
 
 ::
 
-  zgrep -E "#|<Caller>" <*.svdb.vcf.gz>
+  zgrep -E "#|<Caller>" <*.svdb.vcf.gz>
+
+
+
+**Genome Reference Files**
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**How to generate genome reference files for ascatNGS**
+
+Detailed information is available from `ascatNGS <https://github.com/cancerit/ascatNgs>`_ documentation
+
+The file *SnpGcCorrections.tsv* prepared from the 1000 genome SNP panel.
+
+**GC correction file:**
+
+First step is to download the 1000 genome snp file and convert it from .vcf to .tsv. The detailed procedure to for this step is available from `ascatNGS-reference-files <https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs>`_ (Human reference files from 1000 genomes VCFs)
+
+.. code-block::
+
+    export TG_DATA=ftp://ftp.ensembl.org/pub/grch37/release-83/variation/vcf/homo_sapiens/1000GENOMES-phase_3.vcf.gz
+
+
+Followed by:
+
+.. code-block::
+
+    curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\
+    perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/);\
+    next if($F[0] eq $l_c && $F[1]-1000 < $l_p); $F[7]=~m/MAF=([^;]+)/;\
+    next if($1 < 0.05); printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1];\
+    $l_c=$F[0]; $l_p=$F[1];' > SnpPositions_GRCh37_1000g.tsv
+
+
+--or--
+
+.. code-block::
+
+    curl -sSL $TG_DATA | zgrep -F 'E_Multiple_observations' | grep -F 'TSA=SNV' |\
+    perl -ane 'next if($F[0] !~ m/^\d+$/ && $F[0] !~ m/^[XY]$/); $F[7]=~m/MAF=([^;]+)/;\
+    next if($1 < 0.05); next if($F[0] eq $l_c && $F[1]-1000 < $l_p);\
+    printf "%s\t%s\t%d\n", $F[2],$F[0],$F[1]; $l_c=$F[0]; $l_p=$F[1];'\
+    > SnpPositions_GRCh37_1000g.tsv
+
+Second step is to use *SnpPositions.tsv* file and generate *SnpGcCorrections.tsv* file, more details see `ascatNGS-convert-snppositions <https://github.com/cancerit/ascatNgs/wiki/Convert-SnpPositions.tsv-to-SnpGcCorrections.tsv>`_
+
+.. code-block::
+
+    ascatSnpPanelGcCorrections.pl genome.fa SnpPositions.tsv > SnpGcCorrections.tsv
+

docs/bioinfo_softwares.rst

@@ -1,5 +1,5 @@
 =================================
-List of bioinformatics software
+Tools and software
 =================================
 
 BALSAMIC ( **version** = 9.0.1 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each

docs/cli_package.rst

@@ -1,7 +1,7 @@
 =============
-CLI reference
+CLI usage
 =============
 
 .. click:: BALSAMIC.commands.base:cli
    :prog: BALSAMIC
-   :show-nested:
+   :nested: full

docs/conf.py

@@ -13,7 +13,7 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("../"))
+sys.path.insert(0, os.path.abspath(".."))
 
 # -- Project information -----------------------------------------------------
 
@@ -31,7 +31,7 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinxcontrib.napoleon",
-    "sphinx_click.ext",
+    "sphinx_click",
     "sphinxarg.ext",
     "recommonmark",
 ]

docs/git_etiquette.rst

@@ -1,5 +1,5 @@
 =============
-Git Etiquette
+Git etiquette
 =============
 
 It is recommended to follow a system to standardize the commit messages loosely. Following up from commit messages discussed on https://github.com/Clinical-Genomics/development/pull/97 , the format below is recommended for commit messages:

docs/history.rst

@@ -1,4 +1,4 @@
-CHANGELOG
+Changelog
 =========
 
 .. include:: ../CHANGELOG.rst

docs/index.rst

@@ -8,38 +8,23 @@
 
    install
    user_guide
+   cli_package
 
 
 .. toctree::
-   :caption: Resources 
-   :name: resources 
+   :caption: Detailed documentation
+   :name: detailed documentation
    :hidden:
    :maxdepth: 1
 
    balsamic_filters
    balsamic_sv_cnv
    balsamic_annotation
    balsamic_methods
+   history
    bioinfo_softwares
 
 
-.. toctree::
-   :caption: CLI reference 
-   :name: api_cli_reference
-   :hidden:
-   :maxdepth: 1
-
-   cli_package
-
-.. toctree::
-    :caption: Other Info
-    :name: other_info 
-    :hidden:
-    :maxdepth: 1
-
-    history
-    resources
-
 .. toctree::
     :caption: Development guide
     :name: development_guide
@@ -51,3 +36,4 @@
     README
     semver
     FAQs
+    resources

docs/requirements.txt

@@ -4,7 +4,7 @@ docutils>=0.14,<0.18
 recommonmark==0.7.1
 sphinx==4.2.0
 sphinx-argparse==0.3.1
-sphinx-click==3.0.1
+sphinx-click==3.0.2
 sphinx_rtd_theme==1.0.0
 sphinxcontrib-napoleon==0.7
 furo==2021.10.9

docs/resources.rst

@@ -1,11 +1,8 @@
-===============
+================
 Other resources
-===============
+================
 
 
-Resources
----------
-
 *Main resources including knowledge base and databases necessary for pipeline development*
 
 

docs/snakemake_etiquette.rst

@@ -1,5 +1,5 @@
 ===================
-Snakemake Etiquette
+Snakemake etiquette
 ===================
 
 The bioinformatics core analysis in BALSAMIC is defined by set of rules written as a Snakemake rules (``*.rule``) and Snakemake