nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
3.8
). The latest
stable release is
3.19.0
.
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$
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
Save FastQ files after merging re-sequenced libraries in the results directory.
boolean
Options for processing reads with unique molecular identifiers
Enable UMI-based read deduplication.
boolean
UMI pattern to use. Can be either ‘string’ (default) or ‘regex’.
string
string
Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run.
boolean
The UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.
string
Generate output stats when running “umi_tools dedup”.
boolean
After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.
integer
If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.
boolean
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
If this option is specified, FastQ files split by reference will be saved in the results directory.
boolean
Skip BBSplit for removal of non-reference genome reads.
boolean
true
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
${projectDir}/assets/rrna-db-defaults.txt
If this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.
boolean
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
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
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
If generated by the pipeline save the STAR index in the results directory.
boolean
Directory / URL base for iGenomes references.
string
s3://ngi-igenomes/igenomes
Do not load the iGenomes reference config.
boolean
Options to adjust read trimming criteria.
Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).
integer
Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).
integer
Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.
integer
Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.
integer
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
Skip the adapter trimming step.
boolean
Save the trimmed FastQ files in the results directory.
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
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
Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
boolean
Save the intermediate BAM files from the alignment step.
boolean
Skip picard MarkDuplicates step.
boolean
Skip all of the alignment-based processes within the pipeline.
boolean
Options to skip various steps within the workflow.
Specify the RSeQC modules to run.
string
bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
Use vst transformation instead of rlog with DESeq2.
boolean
Skip bigWig file creation.
boolean
Skip StringTie.
boolean
Skip FastQC.
boolean
Skip Preseq.
boolean
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
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
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
Custom config file to supply to MultiQC.
string
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
boolean