nf-core/magmap
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string
^\S+\.csv$
Path to comma-separated file containing information about the genomes to be mapped to.
string
Path to comma-separated file containing a .tsv file which has the same columns as the output from GTDB-Tk. (see docs)
string
Path to txt file with information about genomes in NCBI.
string
./assets/ncbi_genome_infos.csv
Path to .sbt file.
string
Path to comma-separated file containing information from GTDB. For column description, see docs.
string
Path to comma-separated file containing the output from CheckM. For column description, see docs.
string
Activate when you work with single ends reads.
boolean
Email address for completion summary.
string
^([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.
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Option for QC steps
Skip all QC steps except for MultiQC.
boolean
Skip FastQC.
boolean
All the trim option are listed below
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
string
Instructs Trim Galore to remove bp from the 5’ end of read 2 (or single-end reads).
string
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
string
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
string
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
string
Save the trimmed FastQ files in the results directory.
boolean
Skip the adapter trimming step.
boolean
All the options you can use for BBmap or BBduk)
Instructs BBduk to use a fasta file to filter away sequences before running further analysis.
string
Minimal identity for BBmap
number
0.9
Save bam output file
boolean
Save ref folder containing the reference index
boolean
Save genomes concatenated file
boolean
Prokka option
Enable to save prokka output. Default: false
boolean
FeatureCounts option
Specify which features to count
string
CDS,rRNA,tRNA,tmRNA
All the options available for Sourmash
Activate Sourmash
boolean
K-mer size used by Sourmash
integer
21
Save Sourmash outuput
boolean
Saves query sequences that do not have a match in the database, allowing further analysis of unclassified data.
boolean
true
Stores all database signatures that matched the query, enabling reuse without re-running the search.
boolean
true
Saves prefetched signatures, which are database entries that share similarity with the query but may not be full matches, for further inspection.
boolean
true
Outputs a CSV file summarizing the prefetched results, including metadata about retrieved signatures.
boolean
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 config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
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
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string