nf-core/sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
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$
Path to comma-separated file containing the sample names for the desired paired comparisons.
string
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)?$
Do not load the iGenomes reference config.
boolean
true
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes
Specify aligner to be used to map reads to reference genome.
string
Specify the program to use for read trimming
string
Path to directory or tar.gz archive for pre-built BWA index.
string
If generated by the pipeline save the aligner index (e.g. BWA) in the results directory.
boolean
Path to directory or tar.gz archive for pre-built bowtie2 index.
string
If generated by the pipeline save the BWA index in the results directory.
boolean
A BED or GTF file containing regions that should be excluded from all analyses.
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
Less common options for the pipeline, typically set in a config file.
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
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
Specify after which step the pipeline should stop.
string
boolean
Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string
Defines how much the reads should be extended
integer
bw_resolution (expressed in base pairs) for genome coverage calculation (default 1).
integer
1
Method selecte to perform the normalizazion
string
Estimated genome size to performing the normalization
integer
A list of space-delimited chromosome names containing those chromosomes that should be excluded for computing the normalization
string
If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate\u2019s position also has to coincide to ignore a read
boolean
-L options filter the alignments that will be included in the output to only those alignments that match certain criteria.
string
kip alignments with MAPQ smaller than ‘value’ (1 default).
integer
1
If set filter reads based on specific flags. Flags represent various properties of a read, such as whether it’s mapped, paired, or properly aligned (default 1540)
integer
1540
Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example –region chr10 or –region chr10:456700:891000.
string
The number of bins that are sampled from the genome, for which the overlapping number of reads is computed. (Default: 500000)
integer
500000
Deeptools multiBamSummary bam bin size (Default 50000).
integer
Deeptools Correlation Plot statistical calculation method
string
Fragment size parameter for single-end data. When set to a positive value, it enables the —extendReads option in DeepTools, extending reads to the specified length. This parameter is only used for single-end data processing and does not affect paired-end data analysis.
integer
100
Optionally provide chromosome sizes file as input
string
Optionally provide FASTA index (.fai) file as input
string
Path to GTF annotation file.
string
Path to BED file containing gene intervals. This will be created from the GTF file if not specified.
string