This workflow performs read trimming on Accel Amplicon Panel data, using the recommended guidelines provided by Swift
Patrik Smeds (@smeds)
Samples have to be Paired-End Illumina sequences.
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, once available, its DOI.
Configure the workflow according to your needs by editing the config.yaml and the sample sheet samples.tsv.
The following entries are expected in the config file
illuminaclip_file: /path/to/illumina.fa
accel_panels:
panel1:
5p_primer_file: /path/to/5p_primers.fa
3p_primer_file: /path/to/3p_primers.fa
panel2:
5p_primer_file: /path/to/5p_primers.fa
3p_primer_file: /path/to/3p_primers.fa
Example of a sample.tsv file (columns need to be tab separated)
sample panel
sample1 panel1
sample2 panel2
The panel column must contain a panel name that can be found in the accel_panels entry in the config.yaml
Example of a units.tsv file (columns need to be tab separated)
sample unit fq1 fq2
sample1 lane1 /path/to/sample1.R1.fastq /path/to/sample1.R2.fastq
sample2 lane1 /path/to/sample2.R1.fastq /path/to/sample2.R2.fastq
There cane be multiple lanes or replicates for the same sample.
Test your configuration by performing a dry-run via
snakemake -n
Execute the workflow locally via
snakemake --cores $N
using $N cores or run it in a cluster environment via
snakemake --cluster qsub --jobs 100
or
snakemake --drmaa --jobs 100
See the Snakemake documentation for further details.