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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
Path to comma-separated file containing information about the genomes to be mapped to.
stringYou will need to create a file with information about the genomes you want to map to before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. Columns are: accno, genomes_fna, genomes_gff. Please see the documentation for more information.
Path to comma-separated file containing a .tsv file which has the same columns as the output from GTDB-Tk. (see docs)
stringYou will need to use or create a file with information about the genomes' taxonomy you want to map to before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. Columns are: gtdb_genome_representative, gtdb_representative, gtdb_taxonomy. Please see the documentation for more information.
Path to txt file with information about genomes in NCBI.
string./assets/ncbi_genome_infos.csvYou can provide either a file with paths of files containing information about genomes from NCBI (refseq and genebank) or a comma separated paths. These files can be use directly from https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt and ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt. You can also modify the file to include only the genomes you are interested in.
Path to .sbt file.
stringPath to comma-separated file containing information from GTDB. For column description, see docs.
stringYou will need to use or create a file with information about the genomes' taxonomy you want to map to before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 9 columns, and a header row. Columns are: accno, checkm_completeness, checkm_contamination, checkm_strain_heterogeneity, contig_count, genome_size, gtdb_genome_representative, gtdb_representative, gtdb_taxonomy.
Path to comma-separated file containing the output from CheckM. For column description, see docs.
stringYou will need to use or create a file with information about the genomes' statistics you want to map to before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row. Columns are: checkm_completeness, checkm_contamination, contig_count, checkm_strain_heterogeneity, genome_size. Please see the documentation for more information.
Activate 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})$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.
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/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 this parameter.
Institutional 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.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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