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Merge pull request #51 from StevenWingett/pre_release
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‎.github/workflows/git_actions.yml

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# Controls when the action will run. Triggers the workflow on push or pull request
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on:
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push:
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branches: [ master, pre_release ]
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branches: [ master ]
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pull_request:
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branches: [ master, pre_release ]
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branches: [ master ]
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:

‎README.txt

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https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen
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Full documentation on using the software is provided at:
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https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html
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https://stevenwingett.github.io/FastQ-Screen/
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The codebase is maintained at:
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https://github.com/StevenWingett/FastQ-Screen

‎RELEASE_NOTES.txt

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Release notes for FastQ Screen v0.15.2 (26 January 2022)
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--------------------------------------------------------
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Updated documentation
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Provided details on the genomes downloaded with the
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command --get_genomes for possible future reference.
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Release notes for FastQ Screen v0.15.1 (11 January 2022)
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--------------------------------------------------------
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Updated contact details.

‎fastq_screen_documentation.md ‎docs/README.md

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‎docs/_config.yml

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theme: jekyll-theme-modernist

‎download_genomes/README.md

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This folder contains details on the downloaded regular (Bowtie2) and bisulphite genomes (Bismark/Bowtie2), should they need to be re-made / uploaded at some future date.
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This folder contains a tree of the files on the remote FTP, the regular/bisulphite configuration files downloaded from the FTP and the FTP location file downloaded from the Babraham server.

‎download_genomes/bisulfite_genomes_config_file/fastq_screen.conf

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# This is a configuration file for fastq_screen
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############
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## Bowtie2 #
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############
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## If the Bowtie2 binary is not in your PATH then you can
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## set this value to tell the program where to find it.
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## Uncomment the line below and set the appropriate location
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#BOWTIE2 /bi/apps/bowtie2/2.3.2/bowtie2
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############
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## BISMARK #
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############
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## If the Bismark binary is not in your PATH then you can
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## set this value to tell the program where to find it.
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## Uncomment the line below and set the appropriate location
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#BISMARK /bi/apps/bismark/bismark
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############
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## Threads #
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############
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## Bowtie can be made to run across multiple CPU cores to
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## speed up your searches. Set this value to the number
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## of cores you want to use for your searches.
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THREADS 7
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##############
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## Databases #
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##############
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## This section allows you to configure multiple databases
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## to search against in your screen. For each database
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## you need to provide a database name (which can't contain
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## spaces) and the location of the bowtie indices which
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## you created for that database.
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##
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## The default entries shown below are only suggested examples
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## you can add as many DATABASE sections as you like, and you
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## can comment out or remove as many of the existing entries
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## as you like.
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#########
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## Human - sequences available from
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## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
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DATABASE Human [FastQ_Screen_Genomes_Path]/Human/GRCh38
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#########
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## Mouse - sequence available from
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## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
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DATABASE Mouse [FastQ_Screen_Genomes_Path]/Mouse/GRCm38
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#########
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## Rat - sequence available from
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## ftp://ftp.ensembl.org/pub/current/fasta/rattus_norvegicus/dna/
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DATABASE Rat [FastQ_Screen_Genomes_Path]/Rat/Rnor_6.0
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############
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# Drosophila
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DATABASE Drosophila [FastQ_Screen_Genomes_Path]/Drosophila_melanogaster/BDGP6
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#########
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## Worm
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DATABASE Worm [FastQ_Screen_Genomes_Path]/C_elegans/WBcel235
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#########
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## Yeast - sequence available from
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## ftp://ftp.ensembl.org/pub/current/fasta/saccharomyces_cerevisiae/dna/
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DATABASE Yeast [FastQ_Screen_Genomes_Path]/Yeast/R64-1-1
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#########
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## Arabidopsis - sequences available from
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DATABASE Arabidopsis [FastQ_Screen_Genomes_Path]/Arabidopsis/TAIR10
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#########
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## Ecoli
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## Sequence available from EMBL accession U00096.2
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DATABASE Ecoli [FastQ_Screen_Genomes_Path]/E_coli/NC_010473
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########
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## PhiX - sequence available from Refseq accession NC_001422.1
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DATABASE PhiX [FastQ_Screen_Genomes_Path]/PhiX/phiX174_plus_SNPs
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‎download_genomes/genome_locations.txt

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ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/
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ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/

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