fix: command in vcf2cytosure rule and update ReadtheDocs #966

khurrammaqbool · 2022-06-22T10:39:38Z

This PR:

Changed: ReadtheDocs
Fixed: command in vcf2cytosure rule

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codecov · 2022-06-22T10:43:05Z

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Merging #966 (0343a09) into develop (6df59a8) will not change coverage.
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@@           Coverage Diff            @@
##           develop     #966   +/-   ##
========================================
  Coverage    99.24%   99.24%           
========================================
  Files           29       29           
  Lines         1714     1714           
========================================
  Hits          1701     1701           
  Misses          13       13

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ivadym

The changes regarding docs looks fine, but it still doesnt render the CLI https://balsamic-docs.readthedocs.io/en/latest/cli_package.html (I tested it in my fork). I will further look into this.

Regarding the content, we discussed some names but maybe you @ashwini06 have some better suggestions how the structure of references/tools should look.

ashwini06 · 2022-06-22T15:22:00Z

Regarding the content, we discussed some names but maybe you @ashwini06 have some better suggestions how the structure of references/tools should look.

@ivadym @khurrammaqbool : I propose that we can change the existing balsamic readthedocs to a more structured one. How about the following structure?

Getting Started

Installation
Short tutorial

Detailed Documentation:

(BALSAMIC) Annotation Resources
(BALSAMIC) Variant Calling Algorithms
(BALSAMIC) Method descriptions
(BALSAMIC) Tools and Softwares
(BALSAMIC) CLI usage
CHANGELOG

Development Guide

Git Etiquette
Snakemake Etiquette
Build doc
Semantic Versioning
FAQs

OTHER INFO:

Knowledge base and Resources

ivadym · 2022-06-22T16:10:15Z

The suggested names look good! We have some new entries in develop branch that I included below and me and @khurrammaqbool liked this structure:

Getting Started

Installation
Short tutorial
CLI usage

Detailed Documentation:

Calling and filtering variants
Structural and Copy number Variants
Annotation resources
Method descriptions
Tools and Software
Changelog
References

Development Guide

Git Etiquette
Snakemake Etiquette
Build doc
Semantic Versioning
FAQs

ashwini06 · 2022-06-22T16:24:04Z

References

The suggested names look good! We have some new entries in develop branch that I included below and me and @khurrammaqbool liked this structure:

Getting Started

Installation

Short tutorial

CLI usage

Detailed Documentation:

Calling and filtering variants

Structural and Copy number Variants

Annotation resources

Method descriptions

Tools and Software

Changelog
> * References

Development Guide

Git Etiquette

Snakemake Etiquette

Build doc

Semantic Versioning

FAQs

References: References doesn't sound like a correct term here, I would suggest keeping this outside of detailed documentation (like Other info), as it is mostly a Knowledge base resource and the text within it includes a huge collection of tools from various resources.

ashwini06 · 2022-06-22T17:05:30Z

@ivadym : Don't forget to add new links to the delivery report, as these Variant Calling Algorithms link will be broken :)

ashwini06

few suggestions

ashwini06 · 2022-06-23T08:05:47Z

docs/balsamic_filters.rst

+     - Analysis type
+     - Somatic/Germline
+     - Variant type
+   * - DNAScope


Suggested change

* - DNAScope

* - DNAscope

ashwini06 · 2022-06-23T08:06:01Z

docs/balsamic_filters.rst

+     - tumor-normal, tumor-only
+     - somatic
+     - SNV, InDel
+   * - TNScope :superscript:`2`


Suggested change

* - TNScope :superscript:`2`

* - TNscope :superscript:`2`

ashwini06 · 2022-06-23T08:06:12Z

docs/balsamic_filters.rst

+     - tumor-normal, tumor-only
+     - somatic
+     - SNV, InDel
+   * - TNScope_umi


Suggested change

* - TNScope_umi

* - TNscope_umi

ashwini06 · 2022-06-23T08:06:26Z

docs/balsamic_filters.rst

+
+: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


Suggested change

:superscript:`2` TNScope output is being merged with TNhaplotyper calls for TO-WGS analysis

:superscript:`2` TNscope output is being merged with TNhaplotyper calls for TO-WGS analysis

ashwini06 · 2022-06-23T08:07:00Z

docs/balsamic_sv_cnv.rst

@@ -1,5 +1,5 @@
 ************************************
-Structural and Copy Number Variants
+Structural and copy-number variants


Suggested change

Structural and copy-number variants

Structural and Copy Number variants

ashwini06 · 2022-06-23T08:11:36Z

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 vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966


Suggested change

* Command in vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966

* Command in vcf2cytosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966

sonarqubecloud · 2022-06-23T08:26:51Z

Kudos, SonarCloud Quality Gate passed!

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khurrammaqbool added 2 commits June 22, 2022 12:37

fix command in vcf2cytosure rule and update ReadtheDocs

c5150c5

fix command in vcf2cytosure rule and update ReadtheDocs

fe30ba1

khurrammaqbool requested a review from hassanfa as a code owner June 22, 2022 10:39

khurrammaqbool self-assigned this Jun 22, 2022

khurrammaqbool requested review from ashwini06 and ivadym as code owners June 22, 2022 10:39

khurrammaqbool mentioned this pull request Jun 22, 2022

CLI reference documentation is not being shown since BALSAMIC 7.0.2 #965

Closed

fix spinx.click

17fdb92

khurrammaqbool mentioned this pull request Jun 22, 2022

Plan for BALSAMIC v10.0 #954

Closed

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ivadym approved these changes Jun 22, 2022

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restructure and reheader ReadtheDocs

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restructure and reheader ReadtheDocs

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khurrammaqbool added 8 commits June 22, 2022 22:43

format header

bf199f9

add SVN small indel table

ccf3b42

format table

6e7edcd

move other resources

51e0e05

reheader

d43bf10

fix space

34675f2

fix manta

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fix manta

51f2133

ashwini06 reviewed Jun 23, 2022

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khurrammaqbool added 2 commits June 23, 2022 10:17

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0343a09

khurrammaqbool merged commit c684d44 into develop Jun 23, 2022

khurrammaqbool deleted the fix/command_in_vcf2cytosure_rule branch June 23, 2022 08:44

This was referenced Jun 23, 2022

[FAILED_ANALYSIS]: Problems with manta in varcall_py27 container #967

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feat: New Release BALSAMIC v10.0.0 #964

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fix: command in vcf2cytosure rule and update ReadtheDocs #966

fix: command in vcf2cytosure rule and update ReadtheDocs #966

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sonarqubecloud bot commented Jun 23, 2022


		: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

	Structural and copy-number variants
	Structural and Copy Number variants

	* Command in vcf2cyosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966
	* Command in vcf2cytosure rule and updated ReadtheDocs https://github.com/Clinical-Genomics/BALSAMIC/pull/966

fix: command in vcf2cytosure rule and update ReadtheDocs #966

fix: command in vcf2cytosure rule and update ReadtheDocs #966

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khurrammaqbool commented Jun 22, 2022

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