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’.
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Options required to basecall and demultiplex samples.
Path to Nanopore run directory files (e.g. ‘fastq_pass/*’) or a basecalled fastq file that requires demultiplexing.
string
Barcode kit used to perform the sequencing e.g. ‘SQK-PBK004’.
string
Require barcode on both ends for basecaller.
boolean
Trim barcodes from the output sequences in the FastQ files from basecaller.
boolean
Device specified in GPU mode using ‘—device’.
string
auto
Cluster options required to use GPU resources (e.g. ‘—part=gpu —gres=gpu:1’).
string
Specify the minimum quality score for qcat in the range 0-100.
integer
60
Search for adapters in the whole read by applying the ‘—detect-middle’ parameter in qcat.
boolean
Skip demultiplexing with qcat.
boolean
Filter reads from FastQ files using NanoLyse
boolean
Fasta file to be filtered against using NanoLyse
string
Options to adjust parameters and filtering criteria for read alignments.
Specifies the aligner to use i.e. ‘minimap2’ or ‘graphmap2’.
string
minimap2
Specifies if the data is strand-specific. Automatically activated when using ‘—protocol directRNA’.
boolean
Save the ‘.sam’ files from the alignment step - not done by default.
boolean
Skip alignment and downstream processes.
boolean
Options to adjust pameters for DNA varinat calling and structural variant calling.
Specifies if variant calling will executed.
boolean
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.
string
medaka
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
.
string
sniffles
Specifies if MNPs will be split into SNPs when using medaka.
boolean
Specifies whether to call variants with pepper_margin_deepvariant in GPU mode.
boolean
Specifies if vcf will be phased when using medaka.
boolean
Skip variant calling.
boolean
Skip structural variant calling.
boolean
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.
string
bambu
Skip transcript quantification and differential analysis.
boolean
Skip differential analysis with DESeq2 and DEXSeq.
boolean
Options to adjust the RNA fusion analysis
Specifies the reference directory for JAFFAL.
string
for_jaffal
Skip differential analysis with DESeq2 and DEXSeq.
boolean
Options to adjust the RNA modification analysis
Skip RNA modification analysis.
boolean
Skip differential modification analysis with xpore.
boolean
Skip m6A detection with m6anet.
boolean
Options to skip various steps within the workflow.
Skip BigBed file generation.
boolean
Skip BigWig file generation.
boolean
Skip NanoPlot.
boolean
Skip FastQC.
boolean
Skip MultiQC.
boolean
Skip all QC steps apart from MultiQC.
boolean
Reference genome related files and options required for the workflow.
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
boolean
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean