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.
1.0.0
). The latest
stable release is
1.1.0
.
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’.
string
FASTQ
Specify if bam file is sorted [false, true]. If false or not specified, bam file will be sorted!
boolean
Specify if sorted bam file should be saved [false, true]. Default: false
boolean
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
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
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to BWA Index genome file.
string
^\S+\.\{alt,amb,ann,bwt,pac,sa\}$
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Save the index reference fasta in the results directory.
boolean
Options to skip various steps within the workflow.
Skip all QC steps except for MultiQC.
boolean
Skip MultiQC step.
boolean
Skip Picard MarkDuplicates and duplicate filtering
boolean
Keep read duplications marked by picard MarkDuplicates.
boolean
Store bam with marked duplicate reads.
boolean
Options to adjust read trimming criteria.
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integer
Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integer
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integer
Skip the adapter trimming step.
boolean
Save the trimmed FastQ files in the results directory.
boolean
Save the merged FastQ files in the results directory.
boolean
Options 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’.
string
circle_map_realign
Parameters used to run AmpliconArchitect. The software needs additional data files not included in
Copy Number Threshold for seeds to be considered by AmpliconArchitect.
string
4.5
Path to the directory containing the mosek license file ‘mosek.lic’.
string
When running AmpliconArchitect, specify reference build [‘GRCh37’, ‘GRCh38]. This is mandatory to match fasta and AA reference build!
string
GRCh38
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
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
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
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean