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$Input sample type. Valid options: ‘DNA’, ‘cDNA’, and ‘directRNA’.
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions 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’.
stringRequire 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’.
booleanSave 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.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
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.
stringSet 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+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$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})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
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
boolean