Whole-genome assemblies and comparative genomics of Fusarium oxysporum f. sp. capsici Pipeline

Nextflow DSL2 pipeline for assembly processing, variant discovery, TE analysis, gene/protein functional annotation, and group-specific variant interpretation.

Main entrypoints

• main.nf
• workflows/preprocess_assembly.nf
• workflows/alignment_variant_calling.nf

Pipeline components

• Read QC and trimming: FastQC, fastp
• Assembly/scaffolding: megahit, ragtag
• Coverage estimation: bwa mem + samtools depth metrics
• Variant calling: Bowtie2, bcftools, SnpEff
• Callable genome workflow: mosdepth + samtools depth + consensus callable BED
• Group-specific variants: strict per-group variant extraction
• TE analysis: RepeatModeler, RepeatMasker (optional McClintock)
• Gene/protein analyses: Liftoff, antiSMASH, BLASTp (MEROPS), dbCAN, SIX BLASTp, TargetP, SignalP, WoLFPSort, optional DeepTMHMM
• Functional annotation for group-specific candidates: EggNOG + PHI-base BLASTp

Required inputs

1) Samplesheet

CSV with header:

sample_id,read1,read2
34,/path/sample34_R1.fastq.gz,/path/sample34_R2.fastq.gz
35,/path/sample35_R1.fastq.gz,/path/sample35_R2.fastq.gz

Default: samplesheet.csv

2) Group map

TSV format:

# sample_id	group
34	GroupB
35	GroupB
41	GroupA
42	GroupA

Default: samplesheets/group_map.tsv

3) External resources

Configure paths in nextflow.config or via CLI:

• BLAST databases (nt/MEROPS/PHI-base)
• SIX query FASTA
• dbCAN database
• EggNOG data directory
• SnpEff DB/JAR
• Tool paths (Conda env/tool binaries)

Running

source ~/miniconda3/etc/profile.d/conda.sh
conda activate /home/sercanozturk/miniconda3/envs/nf-env
nextflow run main.nf --samplesheet_path samplesheet.csv -with-report

Key parameters

• --output_dir
• --samplesheet_path
• --avc_group_map
• --avc_run_group_specific
• --avc_run_group_functional_annotation
• --enable_chr0_blast_append
• --run_mcclintock
• --skip_deeptmhmm

Outputs (high level)

Under results/ (default):

• coverage/
• callable/
• bcftools_callable/
• group_specific_variants/
• eggnog/
• six_blastp/
• dbcan/
• repeatmodeler/, repeatmasker/
• liftoff/, antismash/, blastp/, snpeff/

Notes

• Optional analysis modules can be enabled/disabled with config flags.
• Validate group map and database paths before production runs.