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.gzThe 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})$Specifies if TSS-bigwigs should be generated, additionally to the TSS-bed files
booleanAdjust parameters and filtering criteria for read alignments.
Alignment tool to be used
stringMinimum number of aligned basepairs of a read to be kept
integer15Options for the reference genome indices used to align reads.
Name of iGenomes reference.
stringPath to FASTA genome file.
stringDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanPath to gtf file.
stringPath to star index directory.
stringPath to bowtie index directory.
stringAll generated reference files will be saved to the results folder if this flag is set.
booleanAdjust trimming criteria and sequences.
booleanSet to cut the enzyme binding site at the 5’ end
booleanSelect to cut the linker at the 3’ end
booleanTrim the first G at the 5’ end, if available
booleanArtifacts, generated in the sequencing process, are cut if this flag is not set to false.
booleanSequence of the ecoP15 site at the 5’ end
stringCAGCAGSequence of the linker at the 3’ end
stringTCGTATGCCGTCTTCPath to 5’ end artifacts
string$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.txtDefine 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.
stringWorkflow name.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${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.
integer16Maximum amount of memory that can be requested for any single job.
string128.GBMaximum amount of time that can be requested for any single job.
string240.hParameters 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/masterInstitutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string