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fix: broken cache doc links #1488

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merged 10 commits into from
Oct 17, 2024
Merged

fix: broken cache doc links #1488

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fedcb8f
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Oct 17, 2024
c6fac97
increase max redirects
mathiasbio Oct 17, 2024
e6a1c33
fix typo
mathiasbio Oct 17, 2024
877c763
remove broken link
mathiasbio Oct 17, 2024
677b7d8
apply test
mathiasbio Oct 17, 2024
e9be863
fix links
mathiasbio Oct 17, 2024
02f298c
change links
mathiasbio Oct 17, 2024
f4bb08b
come on work darnit
mathiasbio Oct 17, 2024
4c948b0
change link to article instead
mathiasbio Oct 17, 2024
46e56b0
remove branch for lychee actions
mathiasbio Oct 17, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/urls_check.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
id: git_checkout
uses: actions/checkout@v3
- name: Link Checker
uses: lycheeverse/lychee-action@v1.8.0
uses: lycheeverse/lychee-action@v2.0.2
with:
args: --verbose './BALSAMIC/constants/cache.py' './docs/*.rst'
args: --max-redirects 10 --verbose './BALSAMIC/constants/cache.py' './docs/*.rst'
fail: true
1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -35,6 +35,7 @@ Changed:
* Lowered minimum AF for TGA from 0.007 to 0.005 https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7 https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Fixed TNscope research VCF filters to either PASS or triallelic site https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Increased maximal amount of redirects for lychee test following links in docs to 10 https://github.com/Clinical-Genomics/BALSAMIC/pull/1488

Removed:
^^^^^^^^
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2 changes: 1 addition & 1 deletion docs/install.rst
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Expand Up @@ -52,7 +52,7 @@ Or if you have repository cloned and want it in editable mode:
Step 2. generate BALSAMIC cache and pull containers
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

First generate your own COSMIC database key via: https://cancer.sanger.ac.uk/cosmic/help/file_download
First generate your own COSMIC database key via: https://cancer.sanger.ac.uk/cosmic/register
The following commands will create and download reference directory at ``~/balsamic_cache`` (change this path if you
want it to be created in another location):

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7 changes: 3 additions & 4 deletions docs/resources.rst
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Expand Up @@ -19,7 +19,7 @@ References and other resources
#. **Cancer genomics workflow**: MGI's CWL Cancer Pipelines. https://github.com/genome/cancer-genomics-workflow/wiki
#. **GIAB**: The priority of GIAB is authoritative characterization of human genomes for use in analytical validation and technology development, optimization, and demonstration. https://github.com/genome-in-a-bottle
#. **dbNSFP**: dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. https://sites.google.com/site/jpopgen/dbNSFP
#. **1000Genomes**: The goal of the 1000 Genomes Project was to find most genetic variants with frequencies of at least 1% in the populations studied. http://www.internationalgenome.org/ Download link: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
#. **1000Genomes**: The goal of the 1000 Genomes Project was to find most genetic variants with frequencies of at least 1% in the populations studied. https://doi.org/10.1093/nar/gkz836 Download link: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
#. **HapMap3**: The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap 3 is the third phase of the International HapMap project. http://www.sanger.ac.uk/resources/downloads/human/hapmap3.html Download link: ftp://ftp.ncbi.nlm.nih.gov/hapmap/
#. **GRCh38.p11**: GRCh38.p11 is the eleventh patch release for the GRCh38 (human) reference assembly. https://www.ncbi.nlm.nih.gov/grc/human Download link: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/
#. **dbVar**: dbVar is NCBI's database of genomic structural variation – insertions, deletions, duplications, inversions, mobile element insertions, translocations, and complex chromosomal rearrangements https://www.ncbi.nlm.nih.gov/dbvar Download link: https://www.ncbi.nlm.nih.gov/dbvar/content/ftp_manifest/
Expand All @@ -30,7 +30,7 @@ References and other resources
Sample datasets
---------------

#. **TCRB**: The Texas Cancer Research Biobank (TCRB) was created to bridge the gap between doctors and scientific researchers to improve the prevention, diagnosis and treatment of cancer. This work occurred with funding from the Cancer Prevention & Research Institute of Texas (CPRIT) from 2010-2014. http://txcrb.org/data.html Article: https://www.nature.com/articles/sdata201610
#. **TCRB**: The Texas Cancer Research Biobank (TCRB) was created to bridge the gap between doctors and scientific researchers to improve the prevention, diagnosis and treatment of cancer. This work occurred with funding from the Cancer Prevention & Research Institute of Texas (CPRIT) from 2010-2014. Article: https://www.nature.com/articles/sdata201610

Relevant publications
---------------------
Expand Down Expand Up @@ -132,11 +132,10 @@ Methods and tools
#. **BreakDancer**: SV detection from paired end reads mapping https://github.com/genome/breakdancer
#. **pIndel**: Detect breakpoints of large deletions, medium sized insertions, inversions, and tandem duplications https://github.com/genome/pindel
#. **VarScan**: Variant calling and somatic mutation/CNV detection https://github.com/dkoboldt/varscan
#. **VEP**: Variant Effect Predictor https://www.ensembl.org/info/docs/tools/vep/index.html
#. **VEP**: Variant Effect Predictor https://github.com/Ensembl/ensembl-vep
#. **Probablistic2020**: Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test https://github.com/KarchinLab/probabilistic2020
#. **2020plus**: Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests https://github.com/KarchinLab/2020plus
#. **vtools**: variant tools is a software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis. https://vatlab.github.io/vat-docs/
#. **vt**: A variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt and https://github.com/atks/vt
#. **CNVnator**: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads. https://github.com/abyzovlab/CNVnator
#. **CNVpytor**: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. https://github.com/abyzovlab/CNVpytor
#. **SvABA**: Structural variation and indel detection by local assembly. https://github.com/walaj/svaba
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