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.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Path to the output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
integer15When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file.
booleanSequencing center information to be added to read group of BAM files.
stringPercentage of minimum number of mapped reads for files to be considered for downstream analysis.
integer5Reference 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)?$This parameter is mandatory if --genome is not specified. If you don't have a bowtie or STAR index available this will be generated for you automatically. Combine with --save_reference to save indices index for future runs.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Path to gtf file.
stringPath to star index directory.
stringPath to bowtie index directory.
stringSpecify the platform used for sequencing.
stringUsed by STAR to generate header in BAM file.
All generated reference files will be saved to the results folder if this flag is set.
booleanSave reads, which couldn't be aligned.
booleanAdjust trimming criteria and sequences.
Save trimmed reads
booleanSet to cut the enzyme binding site at the 5' end
booleantrueSelect to cut the linker at the 3' end
booleantrueTrim the first G at the 5' end, if available
booleantrueArtifacts, generated in the sequencing process, are cut if this flag is not set to false.
booleanSequence of the ecoP15 site at the 5' end
stringCAGCAGSequence of the linker at the 3' end
stringTCGTATGCCGTCTTCPath to 5' end artifacts
string$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 all QC processes.
booleanSkip 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 generation of tag clusters from CTSS.
booleanSkip running RSeQC's read distribution QC step on the clustered CTSS.
booleanSkip MultiQC step
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanEmail 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.
booleanCustom config file to supply to MultiQC.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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|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'
Parameters 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.
string