nf-core/callingcards
A pipeline for processing calling cards data
Hops quantification related parameters
Values with less than or equal to this mapq value will not be counted as transpositions. Defaults to 10
integer10Quality Control metric related parameters
Specify the RSeQC modules to run.
stringread_distributionChoose one of the configured aligners. Defaults to bwamem2.
stringOptions to control how reads are processed prior to alignment
UMITools compliant read 1 barcode pattern. See UMITools documentation
stringUMITools compliant read 2 barcode pattern. See UMITools documentation
stringIf reads are single_end, this option allows the user to crop the R1 read. This occurs after trimming
integerSet to true to gzip fastq files after concatenating (assuming the fastq have been split -- see split_fastq_chunk_size). Default is false, and generally houl should not need to change this as the concat fastqs are intermediate files, easier for downstream processes to use unzipped, and will be deleted when you delete th work directory.
booleansplit_fastq_by_size or split_fastq_by_part may be set, but not both at the same time. These parameters control how many parts the input fastq files are split into for parallel processing on a cluster. See seqkit split2 for more information. By default, split_fastq_by_part is set to 10, which will split every fastq file into 10 parts. If you wish to use split_fastq_by_size, set split_fastq_by_part to null to nullify the default value.
integersplit_fastq_by_size or split_fastq_by_part may be set, but not both at the same time. These parameters control how many parts the input fastq files are split into for parallel processing on a cluster. See seqkit split2 for more information. By default, split_fastq_by_part is set to 10, which will split every fastq file into 10 parts. If you wish to use split_fastq_by_size, set split_fastq_by_part to null to nullify the default value.
integer10Define where the pipeline should find input data and save output data.
This determines which workflow to run based on the organism and method from which the data originates. Current options are 'yeast' and 'mammals'
stringPath to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringSet to true to save intermediate files from the PREPARE_GENOME step, eg genome indicies for a given aligner
booleanSet to true to save intermediate files from the PREPARE_READS step, eg chunked and demultiplexed fastq files
booleanset to true to save intermediate files form the ALIGN step, eg un-indexed and unsorted bam files
booleanReference 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)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Path to GTF annotation file.
stringA bed file which specifies regions to hard mask in genome fasta
string^\S+\.bed$Path to FASTA genome file.
string^\S+\.fai$Additional sequences which will be appended to the genomic fasta file after masking
string^\S+\.fn?a(sta)?(\.gz)?$path to the bwaaln index. only used if aligner is bwaaln. if the aligner is bwaaln and this is not provided, the index is created in the pipeline
stringpath to the bwamem2 index. only used if aligner is bwamem2. if the aligner is bwamem2 and this is not provided, the index is created in the pipeline
stringpath to the bowtie index. only used if aligner is bowtie. if the aligner is bowtie and this is not provided, the index is created in the pipeline
stringpath to the bowtie2 index. only used if aligner is bowtie2. if the aligner is bowtie2 and this is not provided, the index is created in the pipeline
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/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.