parameter_docs.md

Parameters

• Default parameters
• Input/output options
• Data feature options
• Reference genome options
• Quality control options
• Alignment options
• Expression analysis options
• Peak calling options
• Peak merging options
• Methylation analysis options
• Plot options
• Other options

>Default parameters

Tools or packages or methods	Version	Parameters (taking Single-end data as example)
Raw data quality control and preprocessing
fastp	0.19.7	default
FastQC	0.11.8	default
rRNA filtering
HISAT2	2.1.0	hisat2 --summary-file ${sample_name}_rRNA_summary.txt --no-spliced-alignment --no-softclip --norc --no-unal -p ${task.cpus} --dta --un-gz ${sample_id}.fastq.gz -x genome_index -U read1.fastq.gz
Reads alignment
STAR	2.6.1b	STAR --runThreadN ${task.cpus} --readFilesCommand zcat --twopassMode Basic --genomeDir genome_index --readFilesIn read1.fastq.gz --outSAMtype BAM Unsorted --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 20 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 1000000 --outFileNamePrefix ${sample_name} > ${sample_name}_log.txt
HISAT2	2.1.0	hisat2 --summary-file ${sample_name}_hisat2_summary.txt -p ${task.cpus} --dta -x genome_index -U read1.fastq.gz
BWA	0.7.17	bwa aln -t ${task.cpus} -f ${read1.baseName}.sai genome_index read1.fastq.gz <br />bwa samse genome_index ${read1.baseName}.sai read1.fastq.gz
Quality control after alignment
SAMtools	1.9	default for converting sam to bam format followed by sorting and indexing, 20 for mapping quality filtering
RseQC	2.6.4	infer_experiment.py junction_annotation.py bam_stat.py junction_saturation.py inner_distance.py read_distribution.py read_duplication.py
Expression quantification
featureCounts	2.0.0	default, -Q 0 -s 0
Differential expression analysis
DESeq2	1.22.1	default
edgeR	3.26.0	default
Peak calling
MeTPeak	1.0.0	default
MACS2	2.1.2	default, -q 0.01 --keep-dup 5 -f BAM --nomodel
MATK	1.0	default, -q 0.05
Meyer		python scripts
Peak merging
RobustRankAggreg	1.1	R scripts
MSPC	5.4.0	default, -r bio -s 1E-4 -w 1E-2 / -r tec -s 1E-2 -w 1E-1
BEDTools	2.27.1	intersectBed
Peak annotated		Perl scripts
motif searching
HOMER	4.9.1	defalut, -len 5,6,7,8 -S 10 -rna -dumpFasta
methylation quantification
QNB	1.1.11	mode="blind"
MATK	1.0	-quantification
RPKM method	2.27.1	(ip_rpkm+1)/(input_rpkm+1)
Differential methylation analysis
QNB	1.1.11	mode="auto"
MATK	1.0	-diff
DESeq2(GLM)	1.22.1	R scripts, diff.log2fc = peak.log2fc - gene.log2fc
edgeR(GLM)	3.26.0	R scripts, diff.log2fc = peak.log2fc - gene.log2fc
Wilcox-test		R scripts

>Input/output options

Params	Default	Description
--designfile	“$baseDir/test_datasets/inputfiles/designfile_paired.tsv”	A tab-separated table describing the path to the Input files and IP files (FASTQ or BAM format) and the grouping information (like “control” or “treated”). It's recommended to edit by Excel and save as .tsv suffix file.
--comparefile	"$baseDir/test_datasets/inputfiles/comparefile.txt"	A text file that specifies the comparison between two different groups. Other options: "false" for projects without differential analysis; "two_groups" for only two groups in the designfile.
--outdir	"$baseDir/results"	Path to the output directory where the results will be saved.
-profile	docker	Configuration files can contain the definition of one or more profiles. Available options: conda, docker, test

>Data feature options

Params	Default	Description
--single_end	false	"false" for paired_end sequencing; "true" for single_end sequencing.
--gzip	true	Whether FASTQ files are be gzipped.
--stranded	no	"yes" means stranded sequencing data; "no" means unstranded sequncing data; "reverse" means reversely stranded sequencing data.

>Reference genome options

Params	Default	Description
--genome	false	Name of iGenomes reference, eg. "GRCh38"
--fasta	"path/to/xxx.fa"	Path to FASTA genome file.
--gtf	"path/to/xxx.gtf"	Path to GTF annotation file.
--star_index	"path/to/STARIndex"	Path to directory for pre-built STAR index.
--bwa_index	"path/to/BWAIndex"	Path to directory for pre-built BWA index.
--hisat2_index	"path/to/HISTA2Index"	Path to directory for pre-built HISAT2 index.
--tophat2_index	"Path/to/Tophat2Index"	Path to directory for pre-built Tophat2 index.
--rRNA_fasta	"Path/to/rRNA.fa"	Path to directory for rRNA FASTA genome file.
--skip_filterrRNA	false	Skip the process of rRNA cleaning before mapping.

>Quality control options

Params	Default	Description
--skip_fastp	false	Skip fastp and data preprocessing.
--skip_fastqc	false	Skip FastQC.
--skip_rseqc	false	Skip RseQC.
--skip_qc	false	Skip all QC steps except for MultiQC.
--skip_createbedgraph	true	Skip the process of generating bedgraph format files and creatIGVjs

>Alignment options

Params	Default	Description
--aligners	star	Specifies the alignment algorithm to use. Available option: "star" OR "bwa" OR "tophat2" OR "hisat2" OR "none"
--skip_sort	false	Skip the process of sorting BAM files.
--mapq_cutoff	20	Range from 0 to 255, "255" means the pipeline will only keep the unique mapping reads, "0" means keeping all reads.

>Expression analysis options

Params	Default	Description
--featurecount_minMQS	0	Integer giving the minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria.
--expression_analysis_mode	DESeq2	Specifies the tool to do the differential expression analysis. Available options: "DESeq2" OR "edgeR" OR "none"

>Peak calling options

Params	Default	Description
--peakCalling_mode	independence	"group" takes all biological repetitions as a sample,only support MeTPeak and MATK; "independence" takes every sample single.
--peak_threshold	medium	The threshold of peak calling. Available options: "low" OR "medium" OR "high"
--skip_peakCalling	false	Skip the process of peak calling.
--skip_metpeak	false	Skip MeTPeak.
--skip_macs2	false	Skip MACS2.
--skip_matk	false	Skip MATK.
--skip_meyer	false	Skip Meyer.

>Peak merging options

Params	Default	Description
--peakMerged_mode	rank	Specifies the tool to merge all peaks. Available options: "rank" OR "macs2": merging all peaks from different peak callers. "MATK" OR "metpeak" OR "mspc" OR "meyer": taking the results of this tool as a baseline to merge all peaks.

>Methylation analysis options

Params	Default	Description
--methylation_analysis_mode	QNB	Specifies the tool to do the differential methylation analysis. Available options: "MATK" OR "QNB" OR "Wilcox-test" OR "edgeR" OR "DESeq2"
--motif_length	5,6,7,8	Length for HOMER motif searching.
--skip_annotation	false	Skip the process of peak annotation.
--skip_m6Aprediction	false	Skip the process of m6A site predicition.
--skip_diffpeakCalling	false	Skip all differential methylation analysis.
--skip_motif	false	Skip the process of motif searching.

>Plot options

Params	Default	Description
--delfc	0.58	The cutoff of log2 fold change in differential gene filtering.
--dmlfc	0.58	The cutoff of log2 fold change in differential peak filtering.
--cluster_method	single	The method of Hierarchical clustering. Available options: "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid"

>Other options

Params	Default	Description
--name	false	Name for the pipeline run. If not sepcified, nextflow will automatically generate a random mnemonic.
--igenomes_base	“s3://ngi-igenomes/igenomes/”	Directory / URL base for iGenomes references.
--igenomes_ignore	false	Do not load the iGenomes reference config.
--max_cpus	16	Maximum number of CPUs that can be requested for any single job.
--max_memory	128.GB	Maximum amount of memory that can be requested for any single job.
--max_time	240.h	Maximum amount of time that can be requested for any single job.
--help	false	Display help text.
--monochrome_logs	false	Do not use coloured log outputs.
--multiqc_config	“$baseDir/assets/multiqc_config.yaml”	Custom config file to supply to MultiQC.
--tracedir	“${params.outdir}/pipeline_info”	Directory to keep pipeline Nextflow logs and reports.