nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
1.0.0). The latest
stable release is
1.5.0
.
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|tsv|txt)$A CSV file describing sample contrasts
string^\S+\.csv$TSV-format abundance matrix
string^\S+\.(tsv|csv|txt)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringA string to identify results in the output directory
stringstudyA string identifying the technology used to produce the data
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$A text file listing technical features (e.g. spikes)
stringWhen set, use the control features in scaling/ normalisation
booleanRmd report template from which to create the pipeline report
string^\S+\.Rmd$A logo to display in the report instead of the generic pipeline logo
stringdocs/images/nf-core-differentialabundance_logo_light.pngCSS to use to style the output, in lieu of the default nf-core styling
stringassets/nf-core_style.cssA markdown file containing citations to include in the fiinal report
stringCITATIONS.mdColumn in the samples sheet to be used as the primary sample identifier
stringsampleType of observation
stringsampleOptions related to features
Feature ID attribute in the GTF file (e.g. the gene_id field)
stringgene_idFeature name attribute in the GTF file (e.g. the gene symbol field)
stringgene_nameType of feature we have, often ‘gene’
stringgeneOptions related to filtering upstream of differential analysis
Minimum abundance value
integer1Minimum observations that must pass the threshold to retain the row/ feature (e.g. gene).
number1A minimum proportion of observations, given as a number between 0 and 1, that must pass the threshold. Overrides minimum_samples
numberAn optional grouping variable to be used to calculate a min_samples value
stringOptions related to data exploration
Clustering method used in dendrogram creation
stringward.D2Correlation method used in dendrogram creation
stringspearmanNumber of features selected before certain exploratory analyses
integer500Length of the whiskers in boxplots as multiple of IQR. Defaults to 1.5.
number1.5Threshold on MAD score for outlier identification
integer-5How should the main grouping variable be selected? ‘auto_pca’, ‘contrasts’, or a valid column name from the observations table.
stringauto_pcaOptions related to differential operations
The suffix associated tabular differential results tables
string.deseq2.results.tsvThe feature identifier column in differential results tables
stringgene_idThe fold change column in differential results tables
stringlog2FoldChangeThe p value column in differential results tables
stringpvalueThe q value column in differential results tables.
stringpadjMinimum fold change used to calculate differential feature numbers
integer2Maximum q value used to calculate differential feature numbrers
number0.05Where a features file (GTF) has been provided, what attributed to use to name features
stringgene_nameIndicate whether or not fold changes are on the log scale (default is to assume they are)
booleantruetest parameter passed to DESeq()
stringfitType parameter passed to DESeq()
stringsfType parameter passed to DESeq()
string‘minReplicatesForReplace’ parameter passed to DESeq()
integer7useT parameter passed to DESeq2
booleanindependentFiltering parameter passed to results()
booleantruelfcThreshold parameter passed to results()
integeraltHypothesis parameter passed to results()
stringgreaterAbspAdjustMethod parameter passed to results()
stringBHalpha parameter passed to results()
number0.1minmu parameter passed to results()
number0.5variance stabilisation method to use when making a variance stabilised matrix
stringShink fold changes in results?
booleantrueNumber of cores
integer1blind parameter for rlog() and/ or vst()
booleantruensub parameter passed to vst()
integer1000Set to run GSEA to infer differential gene sets in contrasts
booleanPermutation type
stringNumber of permutations
integer1000Enrichment statistic
stringMetric for ranking genes
stringGene list sorting mode
stringGene list ordering mode
stringMax size: exclude larger sets
integer500Min size: exclude smaller sets
integer15Normalisation mode
stringRandomization mode
stringMake detailed geneset report?
booleantrueUse median for class metrics
booleanNumber of markers
integer100Plot graphs for the top sets of each phenotype
integer20Seed for permutation
stringtimestampSave random ranked lists
booleanMake a zipped file with all reports
booleanGene sets in GMT or GMX-format
stringNoneReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringGenome annotation file in GTF format
string^\S+\.gtf(\.gz)?Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanParameters 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.
stringSet 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.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
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
boolean