nf-core/circdna
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
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$Specify input format. Default FASTQ. Options ‘FASTQ’ or ‘BAM’.
stringSpecify if bam file is sorted [false, true]. If false or not specified, bam file will be sorted!
booleanSpecify if sorted bam file should be saved [false, true]. Default: false
booleanThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions to adjust inital circular DNA identifier
Specifies the circular DNA identification algorithm to use - available ‘circle_map_realign’, ‘circle_map_repeats’, ‘circle_finder’, ‘circexplorer2’, and ‘ampliconarchitect’. Multiple circle_identifier’s can be specified with a comma-separated string. E.g. --circle_identifier 'circle_map_realign,unicycler'.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Do not load the iGenomes reference config.
booleanSave the index reference fasta in the results directory.
booleanPath to the directory containg the BWA index files.
stringOptions to skip various steps within the workflow.
Skip all QC steps except for MultiQC.
booleanSkip MultiQC step.
booleanSkip Picard MarkDuplicates and duplicate filtering
booleanKeep read duplications marked by picard MarkDuplicates.
booleantrueStore bam with marked duplicate reads.
booleantrueOptions to adjust read trimming criteria.
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integerInstructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integerInstructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integerInstructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integerSkip the adapter trimming step.
booleanSave the trimmed FastQ files in the results directory.
booleanSave the merged FastQ files in the results directory.
booleanParameters used to run Circle-Map.
Store bam file with read candidates for circle-map circular dna calling.
booleanParameters used to run Circle_finder.
Store bed files created during Circle_finder run.
booleanParameters used to run Unicycler.
Store fastq intermediate files created during Uniycler run.
booleanparameters used to run ampliconarchitect. The software needs additional data files not included in
Copy Number Threshold for seeds to be considered by AmpliconArchitect.
string4.5Path to the directory containing the mosek license file ‘mosek.lic’.
stringWhen running AmpliconArchitect, specify reference build [‘GRCh37’, ‘GRCh38’, ‘mm10’]. This is mandatory to match fasta and AA reference build!
stringPath to cnn file inside the AmpliconArchitect Data Repository of the respective reference genome. By default it uses the ‘aa_data_repo’ and the ‘reference_build’ input to construct the file path.
stringParameters 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.
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|d|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
boolean