nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Define where the pipeline should find input data and save output data.
Path to the sample sheet (CSV) containing metadata about the experimental samples.
string
^\S+\.csv$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
^[a-zA-Z0-9_\-\.]+$
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to GTF annotation file.
string
^\S+\.gtf(\.gz)?$
Path to GFF3 annotation file.
string
^\S+\.gff(\.gz)?$
Path to BED file containing gene intervals. This will be created from the GTF file if not specified.
string
^\S+\.bed(\.gz)?$
Path to FASTA transcriptome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences.
string
^\S+\.fn?a(sta)?(\.gz)?$
Splice sites file required for HISAT2.
string
Path to directory or tar.gz archive for pre-built STAR index.
string
Path to directory or tar.gz archive for pre-built HISAT2 index.
string
Path to directory or tar.gz archive for pre-built RSEM index.
string
Path to directory or tar.gz archive for pre-built Salmon index.
string
Path to directory or tar.gz archive for pre-built Kallisto index.
string
Minimum memory required to use splice sites and exons in the HiSAT2 index build process.
string
200.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Specify if your GTF annotation is in GENCODE format.
boolean
By default, the pipeline uses the gene_name
field to obtain additional gene identifiers from the input GTF file when running Salmon.
string
gene_name
Define the attribute type used to group features in the GTF file when running Salmon.
string
gene_id
The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts.
string
gene_biotype
By default, the pipeline assigns reads based on the ‘exon’ attribute within the GTF file.
string
exon
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Options to adjust read trimming criteria.
Specifies the trimming tool to use - available options are ‘trimgalore’ and ‘fastp’.
string
Extra arguments to pass to Trim Galore! command in addition to defaults defined by the pipeline.
string
Extra arguments to pass to fastp command in addition to defaults defined by the pipeline.
string
Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.
integer
10000
Options for filtering reads prior to alignment
Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit. You have to also explicitly set --skip_bbsplit false
if you want to use BBSplit.
string
Path to directory or tar.gz archive for pre-built BBSplit index.
string
Path to directory or tar.gz archive for pre-built sortmerna index.
string
Enable the removal of reads derived from ribosomal RNA using SortMeRNA.
boolean
Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.
string
${projectDir}/workflows/rnaseq/assets/rrna-db-defaults.txt
Options for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
boolean
Specifies the tool to use for UMI deduplication - available options are ‘umitools’ and ‘umicollapse’.
string
UMI pattern to use. Can be either ‘string’ (default) or ‘regex’.
string
string
The UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.
string
The UMI barcode pattern to use if the UMI is located in read 2.
string
After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.
integer
The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software.
string
^\S+$
Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying the reads with the same mapping position, but treat similar yet nonidentical UMIs differently.
string
Generate output stats when running “umi_tools dedup”.
boolean
Options to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are ‘star_salmon’, ‘star_rsem’ and ‘hisat2’.
string
Specifies the pseudo aligner to use - available options are ‘salmon’. Runs in addition to ‘—aligner’.
string
Kmer length passed to indexing step of pseudoaligners
integer
31
Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
boolean
When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file.
boolean
Override Salmon library type inferred based on strandedness defined in meta object.
string
Minimum percentage of uniquely mapped reads below which samples are removed from further processing.
number
5
Sequencing center information to be added to read group of BAM files.
string
Perform reference-guided de novo assembly of transcripts using StringTie i.e. dont restrict to those in GTF file.
boolean
Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline. Only available for the STAR-Salmon route.
string
Extra arguments to pass to Salmon quant command in addition to defaults defined by the pipeline.
string
Extra arguments to pass to Kallisto quant command in addition to defaults defined by the pipeline.
string
In single-end mode Kallisto requires an estimated fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.
integer
200
In single-end mode, Kallisto requires an estimated standard error for fragment length. Specify a default value for that here. TODO: use existing RSeQC results to do this dynamically.
integer
200
The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5.
number
0.8
The difference in fraction of stranded reads assigned to ‘forward’ and ‘reverse’ below which a sample is classified as ‘unstranded’. By default the forward and reverse fractions must differ by less than 0.1 for the sample to be called as unstranded.
number
0.1
Additional output files produces as intermediates that can be saved
Save FastQ files after merging re-sequenced libraries in the results directory.
boolean
If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.
boolean
If this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.
boolean
If this option is specified, FastQ files split by reference will be saved in the results directory.
boolean
If generated by the pipeline save the STAR index in the results directory.
boolean
Save the trimmed FastQ files in the results directory.
boolean
Save the intermediate BAM files from the alignment step.
boolean
Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
boolean
Save read-by-read assignments from Kraken2.
boolean
Save reads that were not given assignment from Kraken2.
boolean
Additional quality control options.
Extra arguments to pass to the fq lint command.
string
--disable-validator P001
Use vst transformation instead of rlog with DESeq2.
boolean
true
Comma-separated list of RSeQC modules to run.
string
bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
Tool to use for detecting contaminants in unaligned reads - available options are ‘kraken2’ and ‘kraken2_bracken’
string
Database when using Kraken2/Bracken for contaminant screening.
string
Taxonomic level for Bracken abundance estimations.
string
Options to skip various steps within the workflow.
Skip filtering of GTF for valid scaffolds and/ or transcript IDs.
boolean
Skip the ‘transcript_id’ checking component of the GTF filtering script used in the pipeline. Ensure the GTF file is valid.
boolean
Skip BBSplit for removal of non-reference genome reads.
boolean
true
Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run.
boolean
Skip linting checks during FASTQ preprocessing and filtering.
boolean
Skip the adapter trimming step.
boolean
Skip all of the alignment-based processes within the pipeline.
boolean
Skip all of the pseudoalignment-based processes within the pipeline.
boolean
Skip picard MarkDuplicates step.
boolean
Skip bigWig file creation.
boolean
Skip StringTie.
boolean
Skip FastQC.
boolean
Skip Preseq.
boolean
true
Skip dupRadar.
boolean
Skip Qualimap.
boolean
Skip RSeQC.
boolean
Skip additional featureCounts process for biotype QC.
boolean
Skip DESeq2 PCA and heatmap plotting.
boolean
Skip MultiQC.
boolean
Skip all QC steps except for MultiQC.
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
Do not use coloured log outputs.
boolean
Incoming Webhook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/
Suffix to add to the trace report filename.
string
^[a-zA-Z0-9_\-\.{}]+$