nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
1.6). The latest
stable release is
4.1.0
.
Define where the pipeline should find input data and save output data.
Input FastQ files.
stringSpecifies that the input is single-end reads.
booleanThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Alignment tool to use.
stringOutput information for all cytosine contexts.
booleanSave aligned intermediates to results directory
booleanPresets for working with specific bisulfite library preparation methods.
Preset for working with PBAT libraries.
booleanTurn on if dealing with MspI digested material.
booleanRun bismark in SLAM-seq mode.
booleanPreset for EM-seq libraries.
booleanTrimming preset for single-cell bisulfite libraries.
booleanTrimming preset for the Accel kit.
booleanTrimming preset for the CEGX bisulfite kit.
booleanTrimming preset for the Epignome kit.
booleanTrimming preset for the Zymo kit.
booleanOptions for the reference genome indices used to align reads.
Name of iGenomes reference.
stringPath to FASTA genome file.
stringPath to Fasta index file.
stringPath to a directory containing a Bismark reference index.
stringbwameth index filename base
stringSave reference(s) to results directory
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanBisulfite libraries often require additional base pairs to be removed from the ends of the reads before alignment.
Trim bases from the 5’ end of read 1 (or single-end reads).
integerTrim bases from the 5’ end of read 2 (paired-end only).
integerTrim bases from the 3’ end of read 1 AFTER adapter/quality trimming.
integerTrim bases from the 3’ end of read 2 AFTER adapter/quality trimming
integerSave trimmed reads to results directory.
booleanParameters specific to the Bismark workflow
Run alignment against all four possible strands.
booleanOutput stranded cytosine report during Bismark’s bismark_methylation_extractor step.
booleanTurn on to relax stringency for alignment (set allowed penalty with —num_mismatches).
boolean0.6 will allow a penalty of bp * -0.6 - for 100bp reads (bismark default is 0.2)
number0.6Save unmapped reads to FastQ files
booleanSpecify a minimum read coverage to report a methylation call
integerSupply a .gtf file containing known splice sites (bismark_hisat only).
stringAllow soft-clipping of reads (potentially useful for single-cell experiments).
booleanThe minimum insert size for valid paired-end alignments.
integerThe maximum insert size for valid paired-end alignments.
integerSpecify how many CPUs are required per —multicore for bismark align
integerSpecify how much memory is required per —multicore for bismark align
stringSpecify a minimum read coverage for MethylDackel to report a methylation call.
integerMethylDackel - ignore SAM flags
booleanSave files for use with methylKit
booleanSkip read trimming.
booleanSkip deduplication step after alignment.
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string