Merge pull request #75 from FelixKrueger/dev

Updating docs and Switch over to v8 MGP annotation

.github/workflows/docs.yml

@@ -0,0 +1,20 @@
+name: docs
+on:
+  push:
+    branches:
+      - master
+      - dev
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+      - run: pip install mkdocs-material pillow cairosvg
+      - run: mkdocs gh-deploy --force

CHANGELOG.md

@@ -1,8 +1,14 @@
-## v0.5.0dev
+## v0.6.0 (Release 07 01 2023)
+
+- Restructured the documentation, using `mkdocs`. The new User Guide lives at this address: http://felixkrueger.github.io/SNPsplit/
+
+- Reworked all of SNPsplit to reflect changes of the [Mouse Genomes Project](https://www.mousegenomes.org/). This includes the overdue switch-over to the latest v8 annotation (available [here](https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/)) and the GRCm39 mouse genome build
+
+- Kept the old v5 (and v7) genome build instructions as [legacy documentation](http://felixkrueger.github.io/SNPsplit/genome_prep/legacy/)
 
 ### SNPsplit
 
-Added an option `--single_end` to skip the paired-end auto-detection entirely (which failed for e.g. alignments with STAR [see here](https://github.com/FelixKrueger/SNPsplit/pull/56)).
+- Added an option `--single_end` to skip the paired-end auto-detection entirely (which failed for e.g. alignments with STAR [see here](https://github.com/FelixKrueger/SNPsplit/pull/56))
 
 ### SNPsplit_genome_preparation
 

README.md

@@ -1,25 +1,15 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/snpsplit/README.html)
 
-<p align="center"> <img title="SNPsplit" id="logo_img" src="Images/SNPsplit.png" width=300></p>
+<p align="center"> <img title="SNPsplit" id="logo_img" src="docs/images/SNPsplit.png" width=300></p>
 
 ## Allele-specific alignment sorting
 
+> **See the documentation: https://felixkrueger.github.io/SNPsplit**
+
 **Update December 2022:**
 
 SNPsplit has now been updated to work with new release of the [Mouse Genomes Project](https://www.mousegenomes.org/). This means that it will now assume the GRCm39 mouse genome build by default, and use the latest SNP annotation file (v8: [mgp_REL2021_snps.vcf.gz](https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz)).
 
-### Note for using a UCSC/NCBI genome in conjunction with the VCF file from the Mouse Genomes Project 
-
-Several users have run into problems when using genomes from UCSC or NCBI in conjunction with the VCF file from the Mouse Genomes Project (MGP, https://www.mousegenomes.org/).
-The reason for this is that the MGP uses chromosomal coordinates from Ensembl (i.e. `1, 2, 3, X, MT`) whereas UCSC uses chromosome names that look like this: `chr1, chr2, chr3, chrX, chrM`.
-
-We have recently added a check to the SNPsplit genome preparation script that will bail if a chromosome name discrepancy is detected (https://github.com/FelixKrueger/SNPsplit/issues/4). It is however possible to convert the VCF file into a UCSC compatible version by
-(a) changing the chromosome name from e.g. `1` to `chr1` and (b) adding changing the chromosome names in the ID field of the VCF file headers. It is normally not necessary to change the name of the mitochondrium from `MT` to `chrM` because no SNP positions are recorded for the MT anyway.
-
-Here is a one line `awk` script that does an Ensembl=>UCSC conversion, but you could of course also run an equivalent script in Python or Perl...
-```
-awk '{if($1 ~ "^#") {gsub("contig=<ID=", "contig=<ID=chr"); gsub("contig=<ID=chrMT", "contig=<ID=chrM"); print} else {gsub("^MT", "M"); print "chr"$0}}' mgp_REL2021_snps.vcf.gz
-```
 
 ## Installation
 
@@ -29,16 +19,16 @@ SNPsplit requires the following tools installed and ideally available in the `PA
 - [Samtools](http://samtools.sourceforge.net/)
 
 ## Documentation
-The SNPsplit documentation can be found here: [SNPsplit User Guide](./SNPsplit_User_Guide.md)
+The SNPsplit documentation can be found here: [SNPsplit User Guide](https://felixkrueger.github.io/SNPsplit)
 
 ## Links
 - SNPsplit publication at F1000 Research:
   * https://f1000research.com/articles/5-1479/v2
 
-- Here is a link to the [SNPsplit project site](https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/) at the Babraham Institute.
+- Here is a link to the [SNPsplit project site](https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/) at the Babraham Institute
 
 ## Credits
 
-SNPsplit was written by Felix Krueger, as part of the [Babraham Bioinformatics](https://www.bioinformatics.babraham.ac.uk) group.
+SNPsplit was written by Felix Krueger at [Babraham Bioinformatics](https://www.bioinformatics.babraham.ac.uk), now part of Altos Bioinformatics.
 
-<p align="center"> <img title="Babraham Bioinformatics" id="logo_img" src="Images/bioinformatics_logo.png" width=300></p>
+<p align="center"> <img title="Babraham Bioinformatics" id="logo_img" src="docs/images/bioinformatics_logo.png" width=200></p>

SNPsplit

@@ -23,7 +23,7 @@ use Cwd;
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 ## Reading in a BAM or SAM file
-my $pipeline_version = '0.5.1dev';
+my $pipeline_version = '0.6.0';
 my $parent_dir = getcwd;
 my $full_commandline = join (" ","SNPsplit",@ARGV);
 # warn "Full commandline: $full_commandline\n"; sleep(5);
@@ -1788,8 +1788,8 @@ sub process_commandline{
     SNPsplit - Allele-specific alignment sorting
 
 	        Version: $pipeline_version
-	  Copyright 2014-22 Felix Krueger
-             Babraham Bioinformatics
+	  Copyright 2014-23 Felix Krueger
+             Altos Bioinformatics
        https://github.com/FelixKrueger/SNPsplit