nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions for saving a variety of intermediate files
Save reference(s) to results directory
booleanSave aligned intermediates to results directory
booleanBismark only - Save unmapped reads to FastQ files
booleanSave trimmed reads to results directory.
booleanOptions for the reference genome indices used to align reads.
Name of iGenomes reference.
stringPath to FASTA genome file
string^\S+\.fn?a(sta)?(\.gz)?$Path to Fasta index file.
string^\S+\.fn?a(sta)?.fai$Path to a directory containing a Bismark reference index.
stringbwameth index filename base
stringDo not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Alignment tool to use.
stringPresets 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 Zymo kit.
booleanBisulfite libraries often require additional base pairs to be removed from the ends of the reads before alignment.
In addition to manually specifying bases to be hard-clipped, the workflow has a number of parameter presets:
| Parameter | 5’ R1 Trim | 5’ R2 Trim | 3’ R1 Trim | 3’ R2 Trim |
|---|---|---|---|---|
--pbat | 8 | 8 | 8 | 8 |
--single_cell | 6 | 6 | 6 | 6 |
--accel | 10 | 15 | 10 | 10 |
--zymo | 10 | 15 | 10 | 10 |
Note that you can use the --skip_trimming parameter to skip trimming completely.
Further, --skip_trimming_presets disables setting any presets for hard-clipping, thereby uncoupling trimming from specific alignment modes entirely
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
integerTrim bases below this quality value from the 3’ end of the read, ignoring high-quality G bases
integerDiscard reads that become shorter than INT because of either quality or adapter trimming.
integerSkip presetting trimming parameters entirely
booleanParameters specific to the Bismark workflow
Run alignment against all four possible strands.
booleanOutput stranded cytosine report, following 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)
number0.6Specify a minimum read coverage to report a methylation call
integerIgnore read 2 methylation when it overlaps read 1
booleantrueIgnore methylation in first n bases of 5’ end of R1
integerIgnore methylation in first n bases of 5’ end of R2
integer2Ignore methylation in last n bases of 3’ end of R1
integerIgnore methylation in last n bases of 3’ end of R2
integer2Supply a .gtf file containing known splice sites (bismark_hisat only).
string^\S+\.gtf(\.gz)?$Allow soft-clipping of reads (potentially useful for single-cell experiments).
booleanThe minimum insert size for valid paired-end alignments.
integerThe maximum insert size for valid paired-end alignments.
integerSample is NOMe-seq or NMT-seq. Runs coverage2cytosine.
booleanMerges methylation calls for every strand into a single, context dependent file.
booleanCall methylation in all three CpG, CHG and CHH contexts.
booleanMerges methylation metrics of the Cytosines in a given context.
booleanSpecify a minimum read coverage for MethylDackel to report a methylation call.
integerMethylDackel - ignore SAM flags
booleanSave files for use with methylKit
booleanQualimap configurations
A GFF or BED file containing the target regions which will be passed to Qualimap/Bamqc.
string^\S+\.gff|\.bed(\.gz)?$Targeted sequencing analysis configurations. They need --run_targeted_sequencing to have an effect
A BED file containing the target regions
string^\S+|\.bed(\.gz)?$Run Picard CollectHsMetrics in the targeted analysis
booleanSkip read trimming.
booleanSkip deduplication step after alignment.
booleanSkip FastQC
booleanSkip MultiQC
booleanRun preseq/lcextrap tool
booleanRun qualimap/bamqc tool
booleanRun advanced analysis for targeted methylation kits with enrichment of specific regions
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/methylseq/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string