nf-core/clipseq
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
22.10.6
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Define where the pipeline should find input data and save output data.
Input FastQ files.
string
The output directory where the results will be saved.
string
./results
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
Options for the reference genome indices used to align reads.
Name of iGenomes reference.
string
Organism for small RNA reference.
string
Path to small RNA FASTA file
string
Path to genome FASTA file.
string
Path to genome FASTA index file
string
Path to GTF annotation file
string
Path to genome STAR index
string
Save STAR index if generated within pipeline.
boolean
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
Define sequencing adapters and UMI options
Sequencing adapter for trimming
string
AGATCGGAAGAGC
UMI format to move to FastQ header (optional)
string
False
Deduplicate using UMIs
boolean
true
UMI separator in the FastQ read name
string
:
Define peak callers and peak calling options
Which peakcaller(s) to use
string
Path to iCount segment file
string
iCount half-window setting
integer
3
iCount merge-window setting
integer
3
Paraclu minimum cluster count
integer
10
Paraclu minimum density increase
integer
2
Paraclu maximum cluster length
integer
200
PureCLIP binding characteristics of protein
integer
PureCLIP merge distance
integer
8
PureCLIP chromosomes for HMM training
string
all
Piranha bin size
integer
3
Piranha clustering distance
integer
3
Define motif finding parameters
Perform motif finding
boolean
Sample n peaks for motif finding
integer
1000
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
Boolean whether to validate parameters against the schema at runtime
boolean
true
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
Do not use coloured log outputs.
boolean
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Show all params when using --help
boolean
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^[\d\.]+\s*.(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^[\d\.]+\.*(s|m|h|d)$
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 configs hostname.
string
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string