nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
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./samplesheet.csv^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Input sample type. Valid options: 'DNA', 'cDNA', and 'directRNA'.
stringYou will need to specify a protocol based on the sample input type. Valid options are 'DNA', 'cDNA', and 'directRNA'.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions required to basecall and demultiplex samples.
Path to Nanopore run directory files (e.g. 'fastq_pass/*') or a basecalled fastq file that requires demultiplexing.
stringBarcode kit used to perform the sequencing e.g. 'SQK-PBK004'.
stringIf you would like to perform demultiplexing please specify a barcode kit that can be recognised by qcat:
qcat barcode kit specifications |
description |
|---|---|
Auto |
Auto detect barcoding kit |
RBK001 |
Rapid barcoding kit |
RBK004 |
Rapid barcoding kit v4 |
NBD103/NBD104 |
Native barcoding kit with barcodes 1-12 |
NBD114 |
Native barcoding kit with barcodes 13-24 |
NBD104/NBD114 |
Native barcoding kit with barcodes 1-24 |
PBC001 |
PCR barcoding kits with 12 barcodes |
PBC096 |
PCR barcoding kits with 96 barcodes |
RPB004/RLB001 |
Rapid PCR Barcoding Kit (SQK-RPB004) and Rapid Low Input by PCR Barcoding Kit |
RPB004/LWB001 |
Low Input by PCR Barcoding Kit |
RAB204 |
16S Rapid Amplicon Barcoding Kit with 12 Barcodes |
VMK001 |
Voltrax Barcoding Kit with 4 barcodes |
Require barcode on both ends for basecaller.
booleanTrim barcodes from the output sequences in the FastQ files from basecaller.
booleanDevice specified in GPU mode using '--device'.
stringautoCluster options required to use GPU resources (e.g. '--part=gpu --gres=gpu:1').
stringSpecify the minimum quality score for qcat in the range 0-100.
integer60Search for adapters in the whole read by applying the '--detect-middle' parameter in qcat.
booleanSkip demultiplexing with qcat.
booleanFilter reads from FastQ files using NanoLyse
booleanFasta file to be filtered against using NanoLyse
stringOptions to adjust parameters and filtering criteria for read alignments.
Specifies the aligner to use i.e. 'minimap2' or 'graphmap2'.
stringminimap2Specifies if the data is strand-specific. Automatically activated when using '--protocol directRNA'.
booleanWhen using --protocol/--stranded the following command-line arguments will be set for minimap2 and graphmap2:
nanoseq input |
minimap2 presets |
graphmap2 presets |
|---|---|---|
--protocol DNA |
-ax map-ont | no presets |
--protocol cDNA |
-ax splice | -x rnaseq |
--protocol directRNA |
-ax splice -uf -k14 | -x rnaseq |
--protocol cDNA --stranded |
-ax splice -uf | -x rnaseq |
Save the '.sam' files from the alignment step - not done by default.
booleanSkip alignment and downstream processes.
booleanOptions to adjust pameters for DNA varinat calling and structural variant calling.
Specifies if variant calling will executed.
booleanSpecifies the variant caller that will used to call small variants (available are: medaka, deepvariant, and pepper_margin_deepvariant). Variant calling is only available if '--call_variants' is set and the protocol is set to DNA. Please note deepvariant and pepper_margin_deepvariant are only avaible if using singularity or docker.
stringmedakaSpecifies the variant caller that will be used to call structural variants (available are: sniffles and cutesv). Structural variant calling is only available if '--call_variants' is set and the protocol is set to DNA.
stringsnifflesSpecifies if MNPs will be split into SNPs when using medaka.
booleanSpecifies whether to call variants with pepper_margin_deepvariant in GPU mode.
booleanSpecifies if vcf will be phased when using medaka.
booleanSkip variant calling.
booleanSkip structural variant calling.
booleanOptions to adjust quantification and differential analysis
Specifies the transcript quantification method to use (available are: bambu or stringtie2). Only available when protocol is cDNA or directRNA.
stringbambuSkip transcript quantification and differential analysis.
booleanSkip differential analysis with DESeq2 and DEXSeq.
booleanOptions to adjust the RNA fusion analysis
Specifies the reference directory for JAFFAL.
stringfor_jaffalSkip differential analysis with DESeq2 and DEXSeq.
booleanOptions to adjust the RNA modification analysis
Skip RNA modification analysis.
booleanSkip differential modification analysis with xpore.
booleanSkip m6A detection with m6anet.
booleanOptions to skip various steps within the workflow.
Skip BigBed file generation.
booleanSkip BigWig file generation.
booleanSkip NanoPlot.
booleanSkip FastQC.
booleanSkip MultiQC.
booleanSkip all QC steps apart from MultiQC.
booleanReference genome related files and options required for the workflow.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified.
Path to GTF annotation file.
string^\S+\.gtf(\.gz)?$This parameter is mandatory if --genome is not specified.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.