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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with either 2 [BAM] or 3 [FASTQ] columns, and a header row. See usage docs.
Specify input format. Default FASTQ. Options 'FASTQ' or 'BAM'.
stringDefine which input file formats are used in the pipeline run. Use either --input_format 'FASTQ' or --input_format 'BAM'.
Specify if bam file is sorted [false, true]. If false or not specified, bam file will be sorted!
booleanSet this parameter if you specified --input_format BAM and supplied sorted BAM files. This will skip the samtools sort step.
Specify if sorted bam file should be saved [false, true]. Default: false
booleanSet this parameter if you specified bam files in your samplesheet.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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'.
stringSpecify the circle_identifier branch used. Multiple circle_identifier's can be specified with a comma-separated string. E.g. --circle_identifier 'circle_map_realign,unicycler'.
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Save the index reference fasta in the results directory.
booleanBy default, indexed reference genome files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
Path to the directory containg the BWA index files.
stringThis parameter is optional. If you don't have a BWA index available this will be generated for you automatically.
Options to skip various steps within the workflow.
Skip all QC steps except for MultiQC.
booleanSet this parameter to skip all quality control steps except MultiQC.
Skip MultiQC step.
booleanSet this parameter to skip the MultiQC step.
Skip Picard MarkDuplicates and duplicate filtering
booleanSet this parameter to skip annotating and filtering of duplicates marked by Picard Markduplicates.
Keep read duplications marked by picard MarkDuplicates.
booleantrueSet this parameter to skip filtering of duplicates marked by Picard Markduplicates.
Store bam with marked duplicate reads.
booleantrueSet this parameter to save bam file with marked duplicate reads.
Options 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.
integerThis enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.
Skip the adapter trimming step.
booleanUse this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.
Save the trimmed FastQ files in the results directory.
booleanBy default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
Save the merged FastQ files in the results directory.
booleanBy default, merged FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.
Parameters used to run Circle-Map.
Store bam file with read candidates for circle-map circular dna calling.
booleanSet this parameter to save bam file with reads extracted by circle-map readextractor.
Parameters used to run Circle_finder.
Store bed files created during Circle_finder run.
booleanSet this parameter to save Circle_finder intermediate files.
Parameters used to run Unicycler.
Store fastq intermediate files created during Uniycler run.
booleanSet this parameter to save Uniycler intermediate files.
parameters used to run ampliconarchitect. The software needs additional data files not included in
Absolute path to the downloaded AA data repository. See AmpliconArchitect.
stringSpecify the absolute path to the AmpliconArchitect data repository. See AmpliconArchitect.
Copy Number Threshold for seeds to be considered by AmpliconArchitect.
string4.5Specify the seed copy number threshold.
Path to the directory containing the mosek license file 'mosek.lic'.
stringSpecify the path to the directory containing the mosek license file named mosek.lic. A free academic license can be obtained at Mosek.com.
When running AmpliconArchitect, specify reference build ['GRCh37', 'GRCh38', 'mm10']. This is mandatory to match fasta and AA reference build!
stringSpecify the reference genome build used for alignment of the WGS reads.
Path 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.
stringSpecify path to cnvkit cnn file inside AmpliconArchitect Data Repository.
Parameters 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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.