workflows-datirium/.gitignore at master · Barski-lab/workflows-datirium · GitHub

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# Python temps
__pycache__/
*.py[cod]
*$py.class
build/
dist/
eggs/
.eggs/
*.egg-info/
*.egg
.tox/

# Editor Temps
.*.sw?
*~
\#*\#
.desktop
.vagrant
.DS_Store
._.DS_Store

# editor temp files
.*.sw?

#bioinformatics stuff
*.bam
# Allow test BAM files for ATAC workflows
!my_local_test_data/atac_lrt_step_1/inputs/*.bam
*.sam
*.bt2
*.bai
*.fa
*.fastq
*.fasta
*.gtf
*.tbi
*.vcf
*.fai
*.bed
*.bedGraph
*.bw
*.bigWig
*.amb
*.ann
*.pac
*.refmap

#archives
*.bz2
*.gz
*.zip
*.tar
*.Z

# Logs
logs
*.log

# Runtime data
pids
*.pid
*.seed

# Directory for instrumented libs generated by jscoverage/JSCover
lib-cov

# Coverage directory used by tools like istanbul
coverage

# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
.grunt

# node-waf configuration
.lock-wscript

# Compiled binary addons (http://nodejs.org/api/addons.html)
build/Release

# Dependency directory
# https://www.npmjs.org/doc/misc/npm-faq.html#should-i-check-my-node_modules-folder-into-git-
node_modules

# Debug log from npm
npm-debug.log

# webstorm files
.idea

# VsCode configs
.vscode*
.claude*
.cursorignore
.DS_Store*
.cursor*
.vscode*
*.code-workspace


# Local test files
my_local_test_files/*
CWL_WORKFLOW_TESTING_SPEC.md
heatmap.html
*code-workspace
deseq-lrt-step-1-test-input-updated.yml
deseq-lrt-step-2-test-input-updated.yml

# DESeq test outputs and artifacts
my_local_test_data/**/outputs/**
my_local_test_data/**/*.rds

# Logs generated by automated test harness
test_logs/
my_local_test_data/lrt_step_2_debug/
.history
.cursor