ChIPseq/.gitignore at master · DanielGarbozo/ChIPseq · GitHub

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# ============================================
# GENERAL IGNORE RULES
# ============================================

# macOS
.DS_Store

# Temporary or editor files
*.tmp
*.bak
*.swp
*~
*.log
*.out
slurm_*.out

# Conda / environment files
.env
.venv/
env/
venv/
ENV/

# ============================================
# PIPELINE-SPECIFIC FOLDERS
# ============================================

# Input raw data
fastq/
fastqs/
*.fastq
*.fastq.gz

# Alignment outputs
alignment/
*.sam
*.bam
*.bai
*_sorted.bam
*_sorted.bam.bai
*_named.tmp.bam

# Coverage / normalization
coverage/
*.bw
*.bigwig

# MACS2 peak calling
MACS2output/
*_peaks.*
*_summits.bed
*_model.r
*_treat_pileup.bdg