# =============================================================================
# nf-test ignore patterns for viralmetagenome pipeline
# =============================================================================

# ------------------------------------------------------------------------------
# System files
# ------------------------------------------------------------------------------
.DS_Store

# ------------------------------------------------------------------------------
# MultiQC reports and data
# ------------------------------------------------------------------------------
multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
multiqc/multiqc_data/multiqc.parquet
multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/llms-full.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
multiqc/multiqc_data/fastqc*
multiqc/multiqc_data/multiqc_fastqc.yaml
multiqc/multiqc_data/multiqc_fastqc_1.yaml
multiqc/multiqc_data/multiqc_fastqc_2.yaml
multiqc/multiqc_data/multiqc_general_stats.txt
multiqc/multiqc_data/mosdepth-coverage-per-contig-single.txt
multiqc/multiqc_data/multiqc_samtools_flagstat.yaml
multiqc/multiqc_data/multiqc_samtools_stats.yaml
multiqc/multiqc_data/multiqc_samtools_stats_1.yaml
multiqc/multiqc_data/samtools_alignment_plot.txt
multiqc/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt
multiqc/multiqc_data/samtools-flagstat-dp_Read_counts.txt
multiqc/multiqc_data/samtools-stats-dp.txt
multiqc/multiqc_data/mosdepth*

# ------------------------------------------------------------------------------
# Pipeline info and overview tables
# ------------------------------------------------------------------------------
pipeline_info/*.{html,json,txt,yml}
overview-tables/samples_overview.tsv
overview-tables/contigs_overview-with-iterations.tsv
overview-tables/contigs_overview.tsv
overview-tables/mapping_overview.tsv

# ------------------------------------------------------------------------------
# Preprocessing outputs
# ------------------------------------------------------------------------------
**/fastqc/**_fastqc.{html,zip}
**/fastp/**fastp.html
**/*_good_out_R*.fastq.gz

# ------------------------------------------------------------------------------
# Alignment and mapping outputs
# ------------------------------------------------------------------------------
**/*.bam
**/bam/**

# ------------------------------------------------------------------------------
# Mapping statistics and metrics
# ------------------------------------------------------------------------------
**/mosdepth/**
**/picard/**
**/flagstat/**
**/metrics/stats/**

# ------------------------------------------------------------------------------
# Variant calling outputs
# ------------------------------------------------------------------------------
**/*.mpileup
**/*.qual.txt
**/*filtered.vcf.gz

# ------------------------------------------------------------------------------
# Log files
# ------------------------------------------------------------------------------
**/*.log

# ------------------------------------------------------------------------------
# Assembly outputs - might not have consitent order of sequences
# ------------------------------------------------------------------------------
**/*_good_out.fasta
**/assemblers/*/idxstats/*.idxstats
**/*.combined.fa
**/*logfile.txt

# ------------------------------------------------------------------------------
# Classification and search results
# ------------------------------------------------------------------------------
**/*kaiju.tsv
**/*.classifiedreads.txt
**/*kraken2_host.unclassified*.fastq.gz
**/all_genomes.txt
**/all_genomes.tsv
**/intermediate/blast/**
**/polishing/blast/**
**/intermediate/cluster/*/*.json
**/polishing/**/*clusters.tsv

# ------------------------------------------------------------------------------
# Consensus quality control
# ------------------------------------------------------------------------------
**/prokka/**/*.gbk
**/prokka/**/*.sqn
