Maintainer: Martin Hölzer
Email: [email protected]
- one .fastq file per sample:
--nano 'sample1.fastq'
- paired end illumina:
--illumina 'S_41_17_Cf*.R{1,2}.fastq.gz'
Hybrid data needs to have matching simpleNames such as sample1.fastq.gz
(ONT) and sample1.R{1,2}.fastq.gz
(Illumina).
After pulling this git:
nextflow run main.nf --nano test_data/ERR3662306_1_small.fastq.gz -profile local,docker
or let nextflow pull this git:
nextflow run hoelzer/mgnify-lr --nano ~/.nextflow/assets/hoelzer/mgnify-lr/test_data/ERR3662306_1_small.fastq.gz --output ~/mgnify-lr_output -profile local,docker
to also decontaminate your reads and final assembly just add a --species
like this:
nextflow run hoelzer/mgnify-lr --nano ~/.nextflow/assets/hoelzer/mgnify-lr/test_data/ERR3662306_1_small.fastq.gz --output ~/mgnify-lr_output --species eco -profile local,docker
Currently supported species with auto-download are:
- hsa [Ensembl: Homo_sapiens.GRCh38.dna.primary_assembly]
- mmu [Ensembl: Mus_musculus.GRCm38.dna.primary_assembly]
- eco [Ensembl: Escherichia_coli_k_12.ASM80076v1.dna.toplevel]
Per default Illumina data will be cleaned for phiX phage and Nanopore data for DNA CS (DCS) spike-in. You can deactivate this via the --phix
and --dcs
flags.
This workflow comes with some pre-defined profiles for local execution and execution on a HPC using Conda, Docker, and Singularity. You can combine different profiles to run the pipeline on different systems (local, LSF, SLURM, Cloud) using different technologies (Conda, Docker, Singularity).
For the most basic execution on a local machine using Docker use:
-profile local,docker
If you want to use Conda instead of Docker:
-profile local,conda
If you want to run on a HPC w/ LSF and Singularity use:
-profile lsf,singularity
# In that case you should also adjust --singularityCacheDir, --workdir, --databases to match your HPC environment
Below are execution examples for the test data in this repository. For each command ideel plots show the difference between the raw and polished assembly. Please keep in mind that this is only a small toy sample.
nextflow run main.nf --list --nano test_data/ont.csv --workdir work -profile local,docker --output results/test_ont-only
nextflow run main.nf --list --nano test_data/ont.csv --workdir work -profile local,docker -resume --output results/test_ont-only-clean --index_ont clean/ont/DCS.mmi --index_fna clean/assembly/DCS_FNA.mmi
nextflow run main.nf --list --nano test_data/ont.csv --illumina test_data/ill.csv --workdir work -profile local,docker -resume --output results/test_hybrid-spades
nextflow run main.nf --list --nano test_data/ont.csv --illumina test_data/ill.csv --workdir work -profile local,docker -resume --output results/test_hybrid-spades-clean --index_ont clean/ont/DCS.mmi --index_fna clean/assembly/NC_001422_DCS.mmi --bbduk clean/NC_001422.fna.gz
nextflow run main.nf --list --nano test_data/ont.csv --illumina test_data/ill.csv --workdir work -profile local,docker -resume --output results/test_hybrid-flye --assemblerHybrid flye
nextflow run main.nf --list --nano test_data/ont.csv --illumina test_data/ill.csv --workdir work -profile local,docker -resume --output results/test_hybrid-flye-clean --index_ont clean/ont/DCS.mmi --index_fna clean/assembly/NC_001422_DCS.mmi --bbduk clean/NC_001422.fna.gz --assemblerHybrid flye