Parameters
Path to comma-separated file containing information about the samples in the experiment.
You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Email address for completion summary.
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
The bcl2fastq samplesheet
default: 'https://raw.githubusercontent.com/jianhong/16S_pipeline/assets/samplesheet.csv'silva train set
default: 'https://zenodo.org/record/4587955/files/silva_nr99_v138.1_train_set.fa.gz?download=1'The latest release can be found at: https://www.arb-silva.de/download/arb-files/
silva species assignment
default: 'https://zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz?download=1'The latest release can be found at: https://www.arb-silva.de/download/arb-files/
Name of iGenomes reference.
If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Directory / URL base for iGenomes references.
default: 's3://ngi-igenomes/igenomes'Do not load the iGenomes reference config.
Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
skip demultiplex or not
The process will start from filter and be followed by dada2 processing . The input fastqs must follow the pattern of "*R{1,2}{fastq,fq}.gz"
Parameters used to describe centralised config profiles. These should not be edited.
The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.
Base directory for Institutional configs.
default: 'https://raw.githubusercontent.com/nf-core/configs/master'If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Set the top limit for requested resources for any single job.
If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.
Note that you can not increase the resources requested by any job using these options. For that you will need your own configuration file. See the nf-core website for details.
Maximum number of CPUs that can be requested for any single job.
default: 16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
default: '128.GB'Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
default: '240.h'Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.
Typically these options would be set in a Nextflow config file loaded for all pipeline runs, such as ~/.nextflow/config.
Email address for completion summary, only when pipeline fails.
An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$File size limit when attaching MultiQC reports to summary emails.
default: '25.MB'Directory to keep pipeline Nextflow logs and reports.
default: '${params.outdir}/pipeline_info'Boolean whether to validate parameters against the schema at runtime
default: 1