Parameters configuration

Required

• --sample_sheet (required) - provide the sample_sheet.csv same format as described above.

• --genome_fasta or --bismark_index (required) - provide the full path of the reference genome sequence (.fa or .fasta) or if the index files are already available, use the full path of the bismark index file instead of genome_fasta.

• --outdir (required) - full path of the output directory. Default is ${baseDir}/process_name

Optional

User can change it directly to conf/params.config or add to the nextflow run command.

• --diff_meth_method (optional) - user can select between EdgeR analysis or MethylKit analysis for group-wise differential methylation calculation.

• --compare_str (optional) - provide the string such as Healthy_vs_Disease (for pair-wise comparisons) or all (for multiple pair-wise comparisons). By default, the pipeline will calculate all from the Sample_sheet.csv.

• --coverage_threshold (optional) - for EdgeR calculation, user can set their own coverage_threshold. Default is 10.

• --multiqc_config (optional) - user can configure MultiQC run.

• --multiqc_title (optional) - user can provide MultiQC title.

• --post_processing (optional) - Default is true to run the post-processing steps. Can be set false to avoid it.

• --qualimap_args (optional) - can use qualimap arguments.

Differential methylation analysis (figure specs, post-processing and GO analysis)

• --logfc_cutoff (optional) - to generate the MA plot, Volcano plot and gene ontology analysis, the mean median difference (mmd) or here as logfc. Default is 1.5.

• --pvalue_cutoff (optional) - for MA plot, volcano plot and calculating the significant differentially methylated CpGs from the analysis, the p-value cutoff is applied. The default is 0.05. This cutoff is also applied to estimate the gene ontology analysis

• --hyper_color (optional) - for MA and volcano plot hypermethylation CpGs colors. Default is red.

• --hypo_color (optional) - for MA and Volcano plot hypomethylated CpGs colors. Default is blue.

• --nonsig_color (optional) - for non-significant DMCs (based on the pvalue cutoff). Default is black.

• --top_n(optional) - for GO analysis. To peak top n (Default: 100) differentially methylated CpGs from the EdgeR/methylKit results.