nf-core/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Global parameters for the pipeline.
Path to the samplesheet file used by the pipeline. The file should be a CSV, TSV, JSON or YAML file. Equivalent to the sampleAnnotation parameter in the snakemake pipeline.
string^\S+\.(csv|tsv|json|yaml|yml)$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. Equivalent to the root parameter in the snakemake pipeline.
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringTitle of the project to be displayed on the rendered HTML output
stringName of iGenomes reference. Equivalant to the genomeAssembly parameter in the snakemake pipeline.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file. Equivalent to the genome parameter in the snakemake pipeline.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to FASTA index file.
string^\S+\.fai$Path to NCBI FASTA genome file. Equivalent to the ncbi option in the genome parameter in the snakemake pipeline.
string^\S+\.fn?a(sta)?(\.gz)?$Path to NCBI FASTA index file.
string^\S+\.fai$Path to UCSC FASTA genome file. Equivalent to the ucsc option in the genome parameter in the snakemake pipeline.
string^\S+\.fn?a(sta)?(\.gz)?$Path to UCSC FASTA index file.
string^\S+\.fai$Path to GTF gene annotations file. Equivalent to the geneAnnotation parameter in the snakemake pipeline, with the difference that a file depicting the kev-value pairs is expected here instead.
string^\S+\.tsv$Full path of the file containing HPO terms. If missing, it reads it from our webserver. Refer to files-to-download. Equivalent to the hpoFile parameter in the snakemake pipeline.
string^\S+\.tsv$Export counts options.
A comma-separated list of gene annotations to export.
stringA comma-separated list of aberrant expression and aberrant splicing groups whose counts should not be exported. If empty, all groups are exported.
stringAberrant expression options.
Run aberrant expression analysis.
booleanA comma-separated list of aberrant expression groups to run. If empty, all groups are run.
stringA positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50.
integer1A positive number indicating the minimum FPKM value for a gene to be considered expressed.
integer1Methods to remove sample covariation in OUTRIDER.
stringA number between (0, 1] indicating the maximum FDR an event can have in order to be considered an outlier.
number0.05A non-negative number. Z scores (in absolute value) greater than this cutoff are considered as outliers.
numberAn integer that controls the maximum value that the encoding dimension can take.
integer3An integer that sets the batch size for counting reads within a bam file. If memory issues persist lower the yieldSize.
integer2000000Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file.
string^\S+\.(yaml|yml)$Aberrant splicing options.
Run aberrant splicing analysis.
booleanA comma-separated list of aberrant splicing groups to run. If empty, all groups are run.
stringA positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50.
integer1If true, it forces samples to be recounted.
booleanSet to true only if counting Nanopore or PacBio long reads.
booleanSet to true if non standard chromosomes are to be kept for further analysis.
booleanIf true, no filter is applied. We recommend filtering.
booleanThe minimal read count in at least one sample required for an intron to pass the filter.
integer20The minimum total read count (N) an intron needs to have at the specified quantile across samples to pass the filter. See --as_quantile_for_filtering.
integer10Defines at which percentile the as_quantile_min_expression filter is applied.
number0.05A value of 0.95 means that at least 5% of the samples need to have a total read count N >= as_quantile_min_expression to pass the filter.
The minimal variation (in delta psi) required for an intron to pass the filter.
number0.05Methods to remove sample covariation in FRASER.
stringVersion of FRASER to use.
stringFRASERA non-negative number. Delta psi values greater than this cutoff are considered as outliers. Set to 0.1 when using FRASER2.
number0.3Same as in aberrant expression.
number0.1An integer that controls the maximum value that the encoding dimension can take.
integer6Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file.
string^\S+\.(yaml|yml)$Mono-allelic expression options.
Run mono-allelic expression analysis.
booleanA comma-separated list of mono-allelic expression groups to run. If empty, all groups are run.
stringIf true (recommended), it emits the header warnings of a VCF file when performing the allelic counts
booleanSame as in aberrant expression.
number0.05A number between [0.5, 1) indicating the maximum allelic ratio allele1/(allele1+allele2) for the test to be significant.
number0.8Skip the addition of the allele frequencies from gnomAD
booleanMaximum allele frequency (of the minor allele) cut-off. Variants with AF equal or below this number are considered rare.
number0.001Maximum variant frequency among the cohort.
number0.05Full path to the vcf file used for VCF-BAM matching.
string^\S+\.vcf\.gz$Full path to the index of the vcf file used for VCF-BAM matching.
string^\S+\.tbi$Same as 'groups', but for the VCF-BAM matching
stringfraction (0-1) used to seperate 'matching' samples and 'non-matching' samples comparing the DNA and RNA data during QC.
number0.05Reference genome related files and options required for the workflow.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
Display version and exit.
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.
Email 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.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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.
string