nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
Skip analysis steps
Skip QC steps
booleanSkip vcf creation step
booleanSkip visualisation steps
booleanDefine where the pipeline should find input data and save output data.
Path to samplesheet file containing information about the samples in the experiment.
string^\S+\.(csv|yaml|yml|json)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringCOSMIC username
stringCOSMIC password
stringPath to reference folder
stringgencode version
integerComma-delimited list of tools to run
stringThe length of the reads provided to the pipeline. This is used for the ‘—sjdbOverhang’ option of STAR as read_length - 1. Providing 1 to this option will disable overhang handling.
integer100Path to arriba reference blacklist
string\S+\.tsv$Path to arriba reference cytobands
string\S+\.tsv$Path to arriba reference known fusions
string\S+\.tsv$Path to arriba reference protein domain
string\S+\.gff3$Path to arriba output
string\S+\.tsv$Download references instead of building them (for fusioncatcher and starfusion)
booleanPath to fusioncatcher output
string\S+\.txt$Use limitSjdbInsertNsj with int for fusioncatcher
integer2000000Path to fusioncatcher references
stringFusioncatcher download link
stringUse limitSjdbInsertNsj with int for fusioninspector STAR process
integer1000000Path to a fusion list file built with format GENE1—GENE2
string\S+\.tsv$Path to fusionreport references
stringPath to HGNC database file
string\S+\.txt$Path to HGNC timestamp file for database retrieval
string\S+\.txt$Use QIAGEN instead of SANGER to download COSMIC database
booleanPath to salmon index
stringPath to starfusion output
string\S+\.tsv$Path to starfusion references
stringPath to the cancer introns CSV file to create the CTAT-SPLICING reference with
stringhttps://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz\S+\.tsv\.gz$Path to Dfam HMM database file
string\S+\.hmm$Path to Dfam H3F database file
string\S+\.h3f$Path to Dfam H3I database file
string\S+\.h3i$Path to Dfam H3M database file
string\S+\.h3m$Path to Dfam H3P database file
string\S+\.h3p$Path to Pfam database file
string\S+\.hmm(\.gz)?$URL to annotation filter rule file
stringhttps://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm^https?://.*Path to starindex references
stringDiscard fusions identified by less than INT tools
integer1Path to fusions to add to the input of fusioninspector
string\S+\.tsv$Options to adjust read trimming criteria.
The amount of bases to trim at the tail of each read, none will be trimmed by default
integerThe amount of bases to trim at the tail of each read for fusioncatcher, none will be trimmed by default
integerPath to adapter fasta file: default: []
string\S+\.f(n|ast)?a$Option to compress BAM files to CRAM.
Output CRAM files instead of BAM files.
booleanReference genome related files and options required for the workflow.
Skip running the analysis, only builds the references
booleanPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to FASTA genome index file.
string^\S+\.fn?ai(\.gz)?$Name of iGenomes reference.
stringPath to GTF genome file.
string^\S+\.gtf?(\.gz)?$Path to GTF genome file.
string^\S+\.refflat?$Path to ribosomal interval list.
string^\S+\.interval_list?$Avoid using Cosmic DB (for example in clinical case applications where a paid license applies.
booleanPath to Fusion Annotation Library to be used in STARFUSION_BUILD.
string\S+\.dat\.gz$Which species dfam should automatically download, default: homo_sapiens.
stringhomo_sapiensVersion of dfam to use
number,nullVersion of pfam to use
number,nullParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringSequencing center
stringSequencing platform
stringWhether to ignore the GTF in STAR alignment
booleanThe maximum amount of RAM to use for sorting the BAM file in STAR. Should by in bits. Setting this value to 0 will use the default amount of STAR.
integer