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.csvYou 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 6 columns, and a header row. See usage docs.
Specifies 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})$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.
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'.
stringIf you would like to skip the basecalling (--skip_basecalling) but still perform the 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 Guppy basecaller.
booleanConfig file used for basecalling that will be passed to Guppy via the '--config' parameter.
stringCannot be used in conjunction with --flowcell and --kit. This can be a local file (e.g. /your/dir/guppy_conf.cfg) or a string specifying a configuration stored in the /opt/ont/guppy/data/ directory of Guppy.
Custom basecalling model file in json format that will be passed to Guppy via the '--model' parameter.
stringCustom basecalling models can be trained with software such as Taiyaki. This can also be a string specifying a model stored in the /opt/ont/guppy/data directory of Guppy.
Whether 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'.
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 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.
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.
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Workflow name.
stringA custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom 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.
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.GBUse 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.hUse 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'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string