nf-core/coproid
Coprolite host Identification pipeline
1.1.1). The latest
stable release is
2.0.0
.
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})$Options for the reference genome indices used to align reads.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanName of candidate species 1
stringName of candidate species 2
stringName of candidate species 3
stringiGenome name for target genome 1
stringiGenome name for target genome 2
stringiGenome name for target genome 3
stringPath to Bowtie2 pre-indexed genome candidate 1
stringPath to Bowtie2 pre-indexed genome candidate 2
stringPath to Bowtie2 pre-indexed genome candidate 3
stringFasta reference of genome candidate 1
stringFasta reference of genome candidate 2
stringFasta reference of genome candidate 3
stringLess common options for the pipeline, typically set in a config file.
Display help text.
booleanEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoName of pipeline run
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSpecifies that the input is single-end reads.
booleanSpecifies 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