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8e9fe02
Add gitignore
ellendejong Nov 2, 2023
156c79e
custom script to run outrider, not working yet.
ellendejong Nov 2, 2023
369cf70
Dockerfile outrider for additional R packages
ellendejong Nov 2, 2023
0e46a46
changes NextflowModules to test and run pipeline
Jan 5, 2024
a01ca9b
changed links to NextflowModules
Jan 5, 2024
e095750
added nextflow.config
Jan 5, 2024
8918ddc
added conf folder witth config files
Jan 5, 2024
5a9e228
added main.nf and yml in outrider
Jan 5, 2024
6dc82eb
edit outrider main.nf
Jan 5, 2024
03407c4
Delete all test files
Jan 9, 2024
fac6d0e
outrider.R with default output dir and correct R script call in main.…
Jan 9, 2024
388de35
Edit path to outrider dir
lonnekevanbrussel Jan 15, 2024
fdaaa3b
Outrider main.nf added tag meta.id and param feature exon/gene
lonnekevanbrussel Feb 6, 2024
fdb3a80
outrider.R added argument feature to use in output tsv file, also as …
lonnekevanbrussel Feb 6, 2024
808c148
Added changes for feature and output in meta.yml file
lonnekevanbrussel Feb 6, 2024
af534ae
Outrider main.nf changed input feature, input refset gene and exon an…
lonnekevanbrussel Feb 19, 2024
cefbef6
Added filtering, findEncodingDim, controlForConfounders, sampleExclus…
lonnekevanbrussel Feb 20, 2024
abae593
versions.yml error
lonnekevanbrussel Feb 20, 2024
22b3d9a
full result, no exclusion mask and fit
lonnekevanbrussel Feb 20, 2024
8648706
Changes regarding separate outrider processes on GENE & EXON level wi…
lonnekevanbrussel Mar 8, 2024
2acf151
Outrider.R additions to generate input files for EMC app. Added separ…
lonnekevanbrussel Jun 18, 2024
ccf831f
forgot }
lonnekevanbrussel Jun 18, 2024
dd36ce0
filter_expression as a separate function in outrider.R
lonnekevanbrussel Jun 19, 2024
3e59c78
chx->CHX in outrider.R
lonnekevanbrussel Jun 19, 2024
5d596e5
fraser module added for aberrant splicing
lonnekevanbrussel Jul 4, 2024
12c1e1c
Instructions for Exon ratio code (un)commenting
lonnekevanbrussel Jul 25, 2024
931a159
added returns for readability, CHX->chx
lonnekevanbrussel Jul 31, 2024
0c330de
Fraser edits for readability and logging
lonnekevanbrussel Jul 31, 2024
21dab56
Newline, enter and genome_gtf passed as argument
lonnekevanbrussel Aug 26, 2024
84a34b1
input format
lonnekevanbrussel Aug 26, 2024
b36dbb9
working file now with gtf file as argument
lonnekevanbrussel Aug 26, 2024
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264 changes: 264 additions & 0 deletions .gitignore
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# History files
.Rhistory
.Rapp.history

# Session Data files
.RData
.RDataTmp

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# RStudio files
.Rproj.user/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
*_cache/
/cache/

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# R Environment Variables
.Renviron

# pkgdown site
docs/

# translation temp files
po/*~

# RStudio Connect folder
rsconnect/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
# For a library or package, you might want to ignore these files since the code is
# intended to run in multiple environments; otherwise, check them in:
# .python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# poetry
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
# This is especially recommended for binary packages to ensure reproducibility, and is more
# commonly ignored for libraries.
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock

# pdm
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
#pdm.lock
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
# in version control.
# https://pdm.fming.dev/#use-with-ide
.pdm.toml

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
!.vscode/launch.json
!.vscode/extensions.json
!.vscode/*.code-snippets

# Local History for Visual Studio Code
.history/

# Built Visual Studio Code Extensions
*.vsix

# General
.DS_Store
.AppleDouble
.LSOverride

# Icon must end with two \r
Icon


# Thumbnails
._*

# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent

# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
!.vscode/launch.json
!.vscode/extensions.json
!.vscode/*.code-snippets

# Local History for Visual Studio Code
.history/

# Built Visual Studio Code Extensions
*.vsix
7 changes: 7 additions & 0 deletions Fraser/1.99.3/environment.yml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::fastqc=0.12.1

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