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
string
path/to/kraken2_db_dir
string
Path to sourcepredict labels file
string
/Users/maxime/Documents/github/coproid/data/sourcepredict/modern_gut_microbiomes_labels.csv
Path to sourcepredict sources file
string
/Users/maxime/Documents/github/coproid/data/sourcepredict/modern_gut_microbiomes_sources.csv
The output directory where the results will be saved.
string
./results
Email 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.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Name of candidate species 1
string
Name of candidate species 2
string
Name of candidate species 3
string
iGenome name for target genome 1
string
iGenome name for target genome 2
string
iGenome name for target genome 3
string
Path to Bowtie2 pre-indexed genome candidate 1
string
Path to Bowtie2 pre-indexed genome candidate 2
string
Path to Bowtie2 pre-indexed genome candidate 3
string
Fasta reference of genome candidate 1
string
Fasta reference of genome candidate 2
string
Fasta reference of genome candidate 3
string
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Name of pipeline run
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.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.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional configs hostname.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Specifies that the input is single-end reads.
boolean
Specifies if AdapterRemoval should merge the paired-end sequences or not.
string
true
Phred quality encoding
integer
Identity threshold to retain read alignment.
number
0.95
Specifies if data is modern (false) or ancient DNA (true).
string
true
Minimum PMDscore to retain read alignment.
integer
3
DNA preparation library type
string
Bowtie settings for sensivity
string
Minimum number of Kraken hits per Taxonomy ID to report
integer
50
Proportion of Endogenous DNA in organism 1 target microbiome
number
0.01
Proportion of Endogenous DNA in organism 2 target microbiome
number
0.01
Proportion of Endogenous DNA in organism 3 target microbiome
number
0.01
Sourcepredict normalization method
string
gmpr
Sourcepredict number of embedding dimenstions
integer
2
Sourcepredict embedding method
string
mds
Sourcepredict number of neighbours
string
all