nf-core/cageseq
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
22.10.6.
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Define where the pipeline should find input data and save output data.
Input FastQ files.
stringdata/*R1.fastq.gzUse this to specify the location of your input FastQ files. For example:
--input 'path/to/data/sample_*_{1,2}.fastq'
Please note the following requirements:
- The path must be enclosed in quotes
- The path must have at least one
*wildcard character - When using the pipeline with paired end data, the path must use
{1,2}notation to specify read pairs.
If left unspecified, a default pattern is used: data/*{1,2}.fastq.gz
The output directory where the results will be saved.
string./resultsEmail 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.
Specifies if TSS-bigwigs should be generated, additionally to the TSS-bed files
booleanAdjust parameters and filtering criteria for read alignments.
Alignment tool to be used
stringMinimum number of aligned basepairs of a read to be kept
integer15Options for the reference genome indices used to align reads.
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.
stringThis parameter is mandatory if --genome is not specified. If you don't have a bowtie1 or STAR index available, they will be generated for you. Combine with --save_reference to save indices for future runs.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/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 file.
stringPath to star index directory.
stringPath to bowtie index directory.
stringAll generated reference files will be saved to the results folder if this flag is set.
booleanAdjust trimming criteria and sequences.
booleanSet to cut the enzyme binding site at the 5' end
booleanSelect to cut the linker at the 3' end
booleanTrim the first G at the 5' end, if available
booleanArtifacts, generated in the sequencing process, are cut if this flag is not set to false.
booleanSequence of the ecoP15 site at the 5' end
stringCAGCAGSequence of the linker at the 3' end
stringTCGTATGCCGTCTTCPath to 5' end artifacts
string$projectDir/assets/artifacts_5end.fastaPath to 3' end artifacts
string$projectDir/assets/artifacts_3end.fastaControl the ribosomal RNA removal through SortMeRNA.
Select to remove ribosoamal reads with SortMeRNA
booleanSelect to save the ribosomal-free reads
booleanPath to SortMeRNA database file
string$projectDir/assets/rrna-db-defaults.txtThe SortMeRNA database file should be a .txt file with a URL/path to a ribisomal fasta file.
Define parameters for paraclu clustering.
Minimum cluster size
integer30Minimum tags per million a cluster has to have
number0.2Skip various steps within the workflow.
Skip FastQC run on input reads.
booleanSkip all trimming steps.
booleanSkip FastQC run on trimmed reads.
booleanSkip alignment step.
booleanSkip samtools stats QC step of aligned reads
booleanSkip steps generating CTSS files including clustering, bed/bigwig and count table output generation.
booleanSkip running RSeQC's read distribution QC step on the clustered CTSS.
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
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.
Workflow name.
stringA custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
File size limit when attaching MultiQC reports to summary emails.
string25.MBIf file generated by pipeline exceeds the threshold, it will not be attached.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Custom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoArguments passed to Nextflow clusterOptions.
stringfalseSet 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.GBUse 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.hUse 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'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base 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 the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string