chipseq/tests/.nftignore at 779ce9a2b4ff97b2024c091d403d81baec118642 · nf-core/chipseq · GitHub

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# === SYSTEM FILES ===
.DS_Store
**/.DS_Store

# === PIPELINE EXECUTION METADATA ===
pipeline_info/*.{html,json,txt,yml}

# === MULTIQC OUTPUTS ===
# MultiQC files contain timestamps, system paths, and run-specific data
multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
multiqc/multiqc_data/BETA-multiqc.parquet
**/multiqc.log
**/multiqc_data.json
**/multiqc_report.html
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}

# === QC TOOL OUTPUTS ===
fastqc/*_fastqc.{html,zip}
**/*_fastqc.html
**/*_val_*_fastqc.html

# === BINARY AND COMPRESSED FILES ===
**/*.{pdf,png,svg,gz,bam,bai,bigWig,zip,RData,rds}

# === TOOL-SPECIFIC METRICS FILES ===
# Picard metrics
**/*.quality_distribution_metrics
**/*.quality_by_cycle_metrics
**/*.insert_size_metrics
**/*.alignment_summary_metrics
**/*.base_distribution_by_cycle_metrics
**/*.MarkDuplicates.metrics.txt

# Trimming reports
**/*_trimming_report.txt

# Generic outputs
**/*.out

# === ANALYSIS RESULTS (FLOATING-POINT VARIATIONS) ===
# DeepTools outputs
**/*.plotFingerprint.raw.txt
**/*.plotFingerprint.qcmetrics.txt
**/*.computeMatrix.vals.mat.tab
**/*.plotHeatmap.mat.tab
**/*.computeMatrix.mat.gz
**/*.plotProfile.tab

# Peak calling and annotation
**/*.annotatePeaks.txt
**/*.boolean.annotatePeaks.txt
**/macs3_peak.summary.txt

# Feature counting
**/*.featureCounts.txt
**/*.featureCounts.txt.summary

# Statistical analysis
**/*.pca.vals.txt
**/*.pca.vals_mqc.tsv
**/*.sample.dists.txt
**/*.sample.dists_mqc.tsv

# === YAML CONFIGURATION FILES ===
**/deeptools_plot_profile_mlib_deeptools.yaml
**/multiqc_deseq2_clustering_1.yaml
**/multiqc_deseq2_pca_1.yaml
**/multiqc_sources.yaml
**/read_distribution_profile.yaml
**/deeptools_fingerprint_plot.yaml
**/deeptools_plot_fingerprint_counts_mlib_deeptools.yaml

# === CHIP-SEQ SPECIFIC OUTPUTS ===
# PhantomPeakQualTools outputs (contain variable correlation data)
**/*.spp_correlation_mqc.tsv
**/*.spp_nsc_mqc.tsv
**/*.spp_rsc_mqc.tsv

# === IGV SESSION FILES ===
# IGV session files contain absolute paths and timestamps
**/igv_files.txt
**/igv_session.xml