nf-core/nanoseq

Path to comma-separated file containing information about the samples in the experiment.

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Path to Nanopore run directory files (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.

Flowcell used to perform the sequencing e.g. ‘FLO-MIN106’. Not required if ‘—guppy_config’ is specified.

Kit used to perform the sequencing e.g. ‘SQK-LSK109’. Not required if ‘—guppy_config’ is specified.

Barcode kit used to perform the sequencing e.g. ‘SQK-PBK004’.

Require barcode on both ends for Guppy basecaller.

Whether to trim the barcodes from the output sequences in the FastQ files from Guppy basecaller.

Config file used for basecalling that will be passed to Guppy via the ‘—config’ parameter.

Custom basecalling model file in json format that will be passed to Guppy via the ‘—model’ parameter.

Whether to demultiplex with Guppy in GPU mode.

Number of ‘—gpu_runners_per_device’ used for Guppy when using ‘—guppy_gpu’.

Number of ‘—cpu_threads_per_caller’ used for Guppy when using ‘—guppy_gpu’.

Basecalling device specified to Guppy in GPU mode using ‘—device’.

Cluster options required to use GPU resources (e.g. ‘—part=gpu —gres=gpu:1’).

Demultiplex fast5 files with demux_fast5.

Specify the minimum quality score for qcat in the range 0-100.

Search for adapters in the whole read by applying the ‘—detect-middle’ parameter in qcat.

Skip basecalling with Guppy.

Skip demultiplexing with Guppy/qcat.

Filter reads from FastQ files using NanoLyse

Fasta file to be filtered against using NanoLyse

Specifies the aligner to use i.e. ‘minimap2’ or ‘graphmap2’.

Specifies if the data is strand-specific. Automatically activated when using ‘—protocol directRNA’.

Save the ‘.sam’ files from the alignment step - not done by default.

Skip alignment and downstream processes.

Specifies if variant calling will executed.

Specifies 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.

Specifies 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.

Specifies if MNPs will be split into SNPs when using medaka.

Specifies whether to call variants with pepper_margin_deepvariant in GPU mode.

Specifies if vcf will be phased when using medaka.

Skip variant calling.

Skip structural variant calling.

Specifies the transcript quantification method to use (available are: bambu or stringtie2). Only available when protocol is cDNA or directRNA.

Skip transcript quantification and differential analysis.

Skip differential analysis with DESeq2 and DEXSeq.

Specifies the reference directory for JAFFAL.

Skip differential analysis with DESeq2 and DEXSeq.

Skip RNA modification analysis.

Skip differential modification analysis with xpore.

Skip m6A detection with m6anet.

Skip BigBed file generation.

Skip BigWig file generation.

Skip pycoQC.

Skip NanoPlot.

Skip FastQC.

Skip MultiQC.

Skip all QC steps apart from MultiQC.