CLI usage Examples
Watch your REGEX
The pipeline does not concatenate the reads. Whenever you use a pattern such as * with unpaired reads the pipeline will process each read separately.
Illumina paired end reads.
This command will select all the read pairs that match the pattern "path-to/SRR*_{1,2}.fastq.gz" and process each pair separately.
nextflow run fmalmeida/ngs-preprocess \
--max_cpus 3 \
--output illumina_paired \
--shortreads "path-to/SRR*_{1,2}.fastq.gz" \
--shortreads_type "paired" \
--fastp_merge_pairs
Note
Since --shortreads will always be a pattern match, example "illumina/SRR9847694_{1,2}.fastq.gz", it MUST ALWAYS be double quoted as the example below.
When using paired end reads it is required that inputs are set with the "{1,2}" pattern. For example: "SRR6307304_{1,2}.fastq". This will properly load reads "SRR6307304_1.fastq" and "SRR6307304_2.fastq"
--fastp_merge_pairs triggers the Fastp module to merge read pairs.
Illumina single end reads
This command will select all the reads that match the pattern "path-to/SRR*.fastq.gz" and process each one separately.
nextflow run fmalmeida/ngs-preprocess \
--max_cpus 3 \
--output illumina_single \
--shortreads "path-to/SRR*.fastq.gz" \
--shortreads_type "single" \
--fastp_additional_parameters " --trim_front1 5 --trim_tail1 5 "
Note
In this example, we pass on an additional parameter (--trim_front1 5 --trim_tail1 5) to Fastp so it trims the reads using a fixed number of bases from the head and tail of reads.
If multiple unpaired reads are given as input at once, pattern MUST be double quoted: "SRR9696*.fastq.gz"
ONT reads (fastq)
This command will select all the reads that match the pattern "path-to/SRR*.fastq.gz" and process each one separately.
nextflow run fmalmeida/ngs-preprocess \
--max_cpus 3 \
--output ONT \
--nanopore_fastq "path-to/SRR*.fastq.gz" \
--lreads_min_length 1000
Note
The parameter --lreads_min_length applies a minimum read length threshold to filter the reads.
Pacbio raw (subreads.bam) reads
This command will select all the reads that match the pattern "path-to/m140905_*.subreads.bam" and process each one separately.
nextflow run fmalmeida/ngs-preprocess \
--max_cpus 3 \
--output pacbio_subreads \
--pacbio_bam "path-to/m140905_*.subreads.bam" \
--pacbio_get_hifi \
-with-report
Note
The parameter --pacbio_get_hifi will make the pipeline try to produce the high fidelity pacbio ccs reads.
-with-report will generate nextflow execution reports.
If multiple reads are given as input at once, pattern MUST be double quoted: "SRR9696*.fastq.gz"
Pacbio raw (legacy .bas.h5 to subreads.bam) reads
nextflow run fmalmeida/ngs-preprocess \
--pacbio_h5 E01_1/Analysis_Results/ \
--output E01_1/Analysis_Results/preprocessed \
--max_cpus 3
Note
This example refers to the SMRT Cell data files available at: https://github.com/PacificBiosciences/DevNet/wiki/E.-coli-Bacterial-Assembly. The path E01_1/Analysis_Results/ is the directory where the legacy *.bas.h5 and *.bax.h5 files are located. The pipeline will load the bas files available in the directory.
Pacbio bas.h5 file and its related bax.h5 files MUST be in the same directory