nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
2.0.1). 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 in the experiment.
string./samplesheet.csv^\S+\.csv$Path to comma-separated file containing information about the samples in the experiment.
stringPath to the output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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 (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.
booleanFilter reads from FastQ files using NanoLyse
booleanFasta file to be filtered against using NanoLyse
Options to adjust parameters and filtering criteria for read alignments.
Specifies the aligner to use i.e. ‘minimap2’ or ‘graphmap2’.
minimap2Specifies 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.
Options 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.
bambuSkip 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.
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 configs hostname.
stringInstitutional 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.
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.
booleanCustom 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
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
boolean