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
integer
10
Quality Control metric related parameters
Specify the RSeQC modules to run.
string
read_distribution
Choose one of the configured aligners. Defaults to bwamem2.
string
Options to control how reads are processed prior to alignment
UMITools compliant read 1 barcode pattern. See UMITools documentation
string
UMITools compliant read 2 barcode pattern. See UMITools documentation
string
If reads are single_end, this option allows the user to crop the R1 read. This occurs after trimming
integer
Set 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.
boolean
split_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.
integer
split_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.
integer
10
Define 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’
string
Path to comma-separated file containing information about the samples in the experiment.
string
^\S+\.csv$
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
Set to true to save intermediate files from the PREPARE_GENOME step, eg genome indicies for a given aligner
boolean
Set to true to save intermediate files from the PREPARE_READS step, eg chunked and demultiplexed fastq files
boolean
set to true to save intermediate files form the ALIGN step, eg un-indexed and unsorted bam files
boolean
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)?$
Do not load the iGenomes reference config.
boolean
Path to GTF annotation file.
string
A 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
string
path 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
string
path 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
string
path 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
string
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|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
Display version and exit.
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
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/