Usage

The pipeline needs to use NextFlow, Singularity/Docker/Conda (for container). Details are given in corresponding pages.

• It is tested locally on Ubuntu server 24.04.2 LTS.
• Tested on HPC (Dardel from PDC, KTH)

Computational Requirements

Software/s Requirements

• Nextflow (>=21.10.3)
• Docker or Singularity (for containerized execution)
• Java (>=8)

Hardware Requirements

• RAM: 6 GB - 200 GB
• CPU: min. 12 cores
• Storage: ~2TB for 24 paired-end samples

Run NextFlow

nextflow run JD2112/TwistMethNext \
    -profile singularity \
    --sample_sheet Sample_sheet_twist.csv \
    --genome_fasta /data/reference_genome/hg38/hg38.fa \ 
    --run_both_methods \
    --gtf_file /data/Homo_sapiens.GRCh38.104.gtf \
    --refseq_file /data/hg38_RefSeq.bed.gz \
    --outdir Results/TwistMethNext_both 

additional options

Run with pre-build reference genome index --bismark_index /data/reference_genome/hg38/

Run only EdgeR --diff_meth_method edger

Run only MethylKit --diff_meth_method methylkit

need annotation files

Remember to add annotation files for different differential methylation analysis

--gtf_file /data/Homo_sapiens.GRCh38.104.gtf for MethylKit

--refseq_file /data/hg38_RefSeq.bed.gz for EdgeR

Help

nextflow run main.nf --help --outdir .

Parameters configuration

User can change the conf/params.config or use the -- flags directly on nextflow command line.

options	Description
--sample_sheet	Path to the sample sheet CSV file (required)
--bismark_index	Path to the Bismark index directory (required unless --genome or --aligned_bams is provided)
--genome	Path to the reference genome FASTA file (required if --bismark_index not provided)
--aligned_bams	Path to aligned BAM files (use this to start from aligned BAM files instead of FASTQ files)
--refseq_file	Path to RefSeq file for annotation (reuired to run both or methylkit)
--gtf_file	Path to GTF file for annotation (reuired to run both or edger)
--outdir	Output directory (default: ./results)
--diff_meth_method	Differential methylation method to use: 'edger' or 'methylkit' (default: edger)
--run_both_methods	Run both edgeR and methylkit for differential methylation analysis (default: false)
--skip_diff_meth	Skip differential methylation analysis (default: false)
--coverage_threshold	Minimum read coverage to consider a CpG site (default: 10)
--logfc_cutoff	Differential methylation cut-off for Volcano or MA plot (default: 1.5)
--pvalue_cutoff	Differential methylation P-value cut-off for Volcano or MA plot (default: 0.05)
--hyper_color	Hypermethylation color for Volcano or MA plot (default: red)
--hypo_cutoff	Hypomethylation color for Volcano or MA plot (default: blue)
--nonsig_color	Non-significant color for Volcano or MA plot (default: black)
--compare_str	Comparison string for differential analysis (e.g. "Group1-Group2")
--top_n_genes	Number of top differentially methylated genes to report for GOplot (default: 100)
--help	Show this help message and exit

MethylKit specific parameters

--assembly - user needs to provide the genome assembly version. Default: hg38

--mc_cores - if required to run on multiple cores. Default: 1

--diff - Differential methylation cutoff value. Default: 0.5

--qvalue - qvalue respect to differential methylation value to identify significant CpGs. Default: 0.05

Other parameters configuration

1. conf/resource.config - for resource settings.
2. conf/base.config - for base settings.
3. nextflow.config - for nextflow run with default setting.
4. dag.config - for DAG configuration settings.

Input File

Sample sheet (CSV format) with sample information

Sample_sheet.csv:

sample_id	group	read1	read2
SN09	Healthy	FASTQ/SN09/SL1_S9_R1_001.fastq.gz	FASTQ/SN09/SL1_S9_R2_001.fastq.gz
SN10	Disease	FASTQ/SN10/SL2_S10_R1_001.fastq.gz	FASTQ/SN10/SL2_S10_R2_001.fastq.gz
SN11	Healthy	FASTQ/SN11/SL3_S11_R1_001.fastq.gz	FASTQ/SN11/SL3_S11_R2_001.fastq.gz
SN12	Disease	FASTQ/SN12/SL4_S12_R1_001.fastq.gz	FASTQ/SN12/SL4_S12_R2_001.fastq.gz
SN13	Healthy	FASTQ/SN13/SL5_S13_R1_001.fastq.gz	FASTQ/SN13/SL5_S13_R2_001.fastq.gz
SN14	Disease	FASTQ/SN14/SL6_S14_R1_001.fastq.gz	FASTQ/SN14/SL6_S14_R2_001.fastq.gz

Results

Here is how the result folder looks like -

.
├── annotate_results
├── bismark_align
├── bismark_deduplicate
├── bismark_genome_preparation
├── bismark_methylation_extractor
├── bismark_report
├── edger_analysis
├── fastqc
├── go_analysis
├── multiqc
├── pipeline_info
├── post_processing
├── qualimap
├── samtools_index
├── samtools_sort
└── trim_galore

bismark alignment with bowtie2

Option	Functionality
-q	Quiet mode: suppresses detailed output.
--score-min L,0,-0.2	Sets a linear minimum score for valid alignments (moderate stringency).
--ignore-quals	Ignores base quality scores during alignment.
--no-mixed	Ensures both ends of paired reads align properly; no single-end alignments.
--no-discordant	Prevents discordant alignments; enforces proper orientation and distance.
--dovetail	Allows overlapping or extended alignments in paired-end reads.
--maxins 500	Sets the maximum allowed distance between paired-end reads to 500 bases.