Usage Examples

Clone or download the repository and call cpipes:

./cpipes --pipeline maggic [options]

Or pull and run directly with Nextflow:

nextflow pull CFSAN-Biostatistics/maggic
nextflow list
nextflow info CFSAN-Biostatistics/maggic
nextflow run CFSAN-Biostatistics/maggic --pipeline maggic --help

Default Run (Short-Read)

cd /data/scratch/$USER
mkdir nf-maggic
cd nf-maggic
./cpipes \
    --pipeline maggic \
    --input /path/to/illumina/fastq/dir \
    --output /path/to/output \
    -profile ahptainer \
    -resume

Long-Read Mode

./cpipes \
    --pipeline maggic_lr \
    --input /path/to/nanopore/fastq/dir \
    --output /path/to/output \
    -profile ahptainer \
    -resume

Single-End Mode (Short-Read)

./cpipes \
    --pipeline maggic \
    --input /path/to/illumina/fastq/dir \
    --output /path/to/output \
    --fq_single_end true \
    --fq_filename_delim_idx 4 \
    -profile ahptainer \
    -resume

Input

The input is a folder containing compressed (.gz) FASTQ files. Sample grouping is automatic based on file names.

For example, with these files:

• KB-01_apple_L001_R1.fastq.gz
• KB-01_apple_L001_R2.fastq.gz
• KB-01_apple_L002_R1.fastq.gz
• KB-01_apple_L002_R2.fastq.gz
• KB-02_mango_L001_R1.fastq.gz
• KB-02_mango_L001_R2.fastq.gz
• KB-02_mango_L002_R1.fastq.gz
• KB-02_mango_L002_R2.fastq.gz

To create two sample groups (apple and mango), split by underscore and group by the first 2 words (--fq_filename_delim_idx 2).

All FASTQ files should have uniform naming patterns.

Output Directory Structure

All outputs are stored in the --output path. The MultiQC report is at maggic-multiqc/CPIPES-Report_multiqc_report.html (or maggic_lr-multiqc/CPIPES-Report_multiqc_report.html for long reads).

Directory	Description
fastp/	Quality-filtered short-read FASTQ and JSON reports
filtlong/	Quality-filtered long-read FASTQ
fastqc/	Long-read quality control reports
megahit/	Metagenome assemblies (short-read FASTA contigs)
flye/	Metagenome assemblies (long-read FASTA contigs)
minimap2/	Alignment BAM files
vamb/	VAMB binning output
semibin2/	SemiBin2 binning output
metabat2/	MetaBat 2 binning output
binette/	Consensus refined bins and quality reports
gtdbtk/	Taxonomic classification results
genomad/	Virus and plasmid detection results
amrfinderplus/	AMR gene detection results
coverm_genome/	Abundance/coverage tables
maggic_results/	Aggregated results TSVs
table_summary/	Summary tables
maggic-multiqc/	MultiQC HTML report (short-read)
maggic_lr-multiqc/	MultiQC HTML report (long-read)