In the nextflowViral package, the pipeline script, bowtieConsensHiCovFromPairedFastq.nf, is written in Nextflow DSL 1 and is thus out-of-date. It generates consensus genomes from paired fastq files mapped to reference at minimum 1X and 25X coverage. To run old_DSL1 files, Nextflow 21.04.3 is required. To run the new pipelines compatible with DSL 2 (under learn_DSL2), Nextflow 23.10.0 and above is required. For setup, Python 3.9.1 and above is required.
To run using input parameters in nextflow.config, simply type the following after installation:
nextflow run bowtieConsensHiCovFromPairedFastq.nf
To run using custom parameters for --querydir and --reference, for example, the folder, my_paired_fastq/, and the reference basename, my_reference/my_genome, type:
nextflow run bowtieConsensHiCovFromPairedFastq.nf --querydir "$PWD/my_paired_fastq/*_R{1,2}*.fastq" --reference $PWD/my_reference/my_genome
Alternatively, to avoid typing complicated filepaths at the command line, simply edit the querydir, reference, intermdir, and/or consensdir in the nextflow.config file.
Prerequisites: bowtie2.2.3.X.X, samtools/1.15.X, BEDTools/2.26.X, bcftools/1.10.X, seqtk/1.3, perl/5.16.X-MT, and nextflow/21.04.X
Required/default input folders are D70_paired_files/ and D70_reference_genome/
ref_180330_Calici36_SureSelectNoro_Capture/ contains .fasta, .sizes, and bowtie2-build .bt2 files
Expected/default output folders are bowtieConsensInterm/ and bowtieConsensOutput/
To set up run environment with required input and output folders and appropriately-formatted files within input folders, enter the command:
python setupFolders.py --input newTest.tar
Here, --input newTest.tar is optional. The default input is bowtieConsensTestFiles.tar.