nrminor
commented
2 weeks ago Also done! Now, when you run nextflow run . --help or nextflow run main.nf --help or nextflow run nrminor/oneroof --help, you get this:
N E X T F L O W ~ version 24.08.0-edge
Launching `./main.nf` [curious_gates] DSL2 - revision: bc848acf05
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88. .88 88 88 88. ... 88 88. .88 88. .88 88
`88888P' dP dP `88888P' dP `88888P' `88888P' dP
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oneroof: Base-, Variant-, and Consensus-calling under One Proverbial Roof
=========================================================================
`oneroof` is a bespoke bioinformatic pipeline that can handle Oxford
Nanopore POD5 basecalling, Illumina paired-end read-merging, read
alignment and variant-calling, variant-effect annotation, consensus
sequence calling, quality reporting, and phylogenetic tree-building, all
under "one roof."
(version 0.1.0)
=========================================================================
Usage:
The typical command for running `oneroof` is as follows:
nextflow run . --prepped_data inputs/ --primer_bed primers.bed --refseq GENOME.fasta --ref_gbk GENOME.gbk -profile containerless
Mandatory arguments:
--refseq The reference sequence to be used for mapping in FASTA format.
Optional arguments:
--primer_bed A bed file of primer coordinates relative to the reference provided with the parameters 'refseq' and 'ref_gbk'.
--ref_gbk The reference sequence to be used for variant annotation in Genbank format.
--fwd_suffix Suffix in the primer bed file denoting whether a primer is forward. Default: '_LEFT'
--rev_suffix Suffix in the primer bed file denoting whether a primer is reverse. Default: '_RIGHT'
--remote_pod5_location A remote location to use with an SSH client to watch for pod5 files in real-time as they are generated. Default: ''
--file_watcher_config Configuration file for remote file monitoring. Default: ''
--pod5_staging Directory where pod5 files are cached as they arrive from the remote location. Default: 'pod5_cache'
--pod5_dir Directory where pod5 files are manually transferred if no remote pod5 location is given. Default: ''
--precalled_staging Directory to watch for Nanopore FASTQs or BAMs as they become available. Default: ''
--prepped_data Location of prepped data if pod5 files are already basecalled and demultiplexed. Default: ''
--illumina_fastq_dir Location of paired-end Illumina FASTQ files to be processed. Default: ''
--model Nanopore basecalling model to apply to the provided pod5 data. Default: 'sup@latest'
--model_cache Directory to cache basecalling models locally. Default: 'work/basecalling_models'
--kit Nanopore barcoding kit used to prepare sequencing libraries. Default: null
--pod5_batch_size How many pod5 files to basecall at once. Default: null
--basecall_max Number of parallel instances of the basecaller to run at once. Default: 1
--max_len Maximum acceptable read length. Default: 12345678910
--min_len Minimum acceptable read length. Default: 1
--min_qual Minimum acceptable average quality for a given read. Default: 20
--secondary Enable secondary alignments for each amplicon. Default: null
--max_mismatch Maximum number of mismatches allowed when finding primers. Default: 0
--downsample_to Desired coverage to downsample to. Default: 0 (no downsampling)
--min_consensus_freq Minimum frequency of a variant base to be included in a consensus sequence. Default: 0.5
--min_haplo_reads Minimum read support to report an amplicon-haplotype. Default: 2
--snpeff_cache Directory to cache a custom snpEff database. Default: 'work/snpEff_cache'
--min_depth_coverage Minimum depth of coverage. Default: 20
--nextclade_dataset Nextclade dataset location. Default: null
--nextclade_cache Directory to cache Nextclade datasets. Default: 'work/nextclade_datasets'
--results Where to place the results. Default: 'results'
--cleanup Whether to clean up the work directory after a successful run. Default: null
Advanced parameters:
--snpEff_config Configuration file for snpEff. Default: 'conf/snpeff.config'
See a great example here: https://github.com/isugifNF/blast/blob/master/main.nf.