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$Path to comma-separated file containing information about the genomes to be mapped to.
stringPath to comma-separated file containing a .tsv file which has the same columns as the output from GTDB-Tk. (see docs)
stringPath to txt file with information about genomes in NCBI.
string./assets/ncbi_genome_infos.csvPath to .sbt file.
stringPath to comma-separated file containing information from GTDB. For column description, see docs.
stringPath to comma-separated file containing the output from CheckM. For column description, see docs.
stringActivate when you work with single ends reads.
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOption for QC steps
Skip all QC steps except for MultiQC.
booleanSkip FastQC.
booleanAll the trim option are listed below
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
stringInstructs Trim Galore to remove bp from the 5’ end of read 2 (or single-end reads).
stringInstructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
stringInstructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
stringInstructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
stringSave the trimmed FastQ files in the results directory.
booleanSkip the adapter trimming step.
booleanAll the options you can use for BBmap or BBduk)
Instructs BBduk to use a fasta file to filter away sequences before running further analysis.
stringMinimal identity for BBmap
number0.9Save bam output file
booleanSave ref folder containing the reference index
booleanSave genomes concatenated file
booleanProkka option
Enable to save prokka output. Default: false
booleanFeatureCounts option
Specify which features to count
stringCDS,rRNA,tRNA,tmRNAAll the options available for Sourmash
Activate Sourmash
booleanK-mer size used by Sourmash
integer21Save Sourmash outuput
booleanSaves query sequences that do not have a match in the database, allowing further analysis of unclassified data.
booleantrueStores all database signatures that matched the query, enabling reuse without re-running the search.
booleantrueSaves prefetched signatures, which are database entries that share similarity with the query but may not be full matches, for further inspection.
booleantrueOutputs a CSV file summarizing the prefetched results, including metadata about retrieved signatures.
booleanParameters 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 config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://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