nf-core/coproid
Coprolite host Identification pipeline
22.10.6.
Learn more.
Define where the pipeline should find input data and save output data.
Path to fastq input files
stringpath/to/kraken2_db_dir
stringPath to sourcepredict labels file
string/Users/maxime/Documents/github/coproid/data/sourcepredict/modern_gut_microbiomes_labels.csvPath to sourcepredict sources file
string/Users/maxime/Documents/github/coproid/data/sourcepredict/modern_gut_microbiomes_sources.csvThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Name of candidate species 1
stringName of candidate species 2
stringName of candidate species 3
stringiGenome name for target genome 1
stringMust be provided if fasta1 is not provided
iGenome name for target genome 2
stringMust be provided if fasta2 is not provided
iGenome name for target genome 3
stringMust be provided if fasta3 is not provided
Path to Bowtie2 pre-indexed genome candidate 1
stringPath to Bowtie2 pre-indexed genome candidate 2
stringPath to Bowtie2 pre-indexed genome candidate 3
stringFasta reference of genome candidate 1
stringMust be provided if genome1 is not provided
Fasta reference of genome candidate 2
stringMust be provided if genome2 is not provided
Fasta reference of genome candidate 3
stringMust be provided if genome3 is not provided
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoName of pipeline run
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$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'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSpecifies that the input is single-end reads.
booleanBy default, the pipeline expects paired-end data. If you have single-end data, you need to specify --single_end on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for --input. For example:
--single_end --input '*.fastq'
It is not possible to run a mixture of single-end and paired-end files in one run.
Specifies if AdapterRemoval should merge the paired-end sequences or not.
stringtruePhred quality encoding
integerIdentity threshold to retain read alignment.
number0.95Specifies if data is modern (false) or ancient DNA (true).
stringtrueMinimum PMDscore to retain read alignment.
integer3DNA preparation library type
stringBowtie settings for sensivity
stringMinimum number of Kraken hits per Taxonomy ID to report
integer50Proportion of Endogenous DNA in organism 1 target microbiome
number0.01Proportion of Endogenous DNA in organism 2 target microbiome
number0.01Proportion of Endogenous DNA in organism 3 target microbiome
number0.01Sourcepredict normalization method
stringgmprSourcepredict number of embedding dimenstions
integer2Sourcepredict embedding method
stringmdsSourcepredict number of neighbours
stringall