nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
1.1.0). The latest
stable release is
3.1.0
.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples you would like to analyse.
string./samplesheet.csvSpecifies the type of data that was sequenced i.e. ‘DNA’, ‘cDNA’ or ‘directRNA’.
stringThe 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})$Options required to basecall and demultiplex samples.
Path to Nanopore run directory (e.g. ‘fastq_pass/’) or a basecalled fastq file that requires demultiplexing. The latter can only be provided in conjunction with the ‘—skip_basecalling’ parameter.
stringFlowcell used to perform the sequencing e.g. ‘FLO-MIN106’. Not required if ‘—guppy_config’ is specified.
stringKit used to perform the sequencing e.g. ‘SQK-LSK109’. Not required if ‘—guppy_config’ is specified.
stringBarcode kit used to perform the sequencing e.g. ‘SQK-PBK004’.
stringRequire barcode on both ends for Guppy basecaller.
booleanConfig file used for basecalling that will be passed to Guppy via the ‘—config’ parameter.
stringCustom basecalling model file in json format that will be passed to Guppy via the ‘—model’ parameter.
stringWhether to demultiplex with Guppy in GPU mode.
booleanNumber of ‘—gpu_runners_per_device’ used for Guppy when using ‘—guppy_gpu’.
integer6Number of ‘—cpu_threads_per_caller’ used for Guppy when using ‘—guppy_gpu’.
integer1Basecalling device specified to Guppy 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 basecalling with Guppy.
booleanSkip demultiplexing with Guppy/qcat.
booleanOptions 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 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 skip various steps within the workflow.
Skip BigBed file generation.
booleanSkip BigWig file generation.
booleanSkip pycoQC.
booleanSkip NanoPlot.
booleanSkip FastQC.
booleanSkip MultiQC.
booleanSkip all QC steps apart from MultiQC.
booleanOptions for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringWorkflow name.
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.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_infoArguments passed to Nextflow clusterOptions.
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.GBMaximum amount of time that can be requested for any single job.
string240.hParameters 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 description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string