nf-core/riboseq
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
1.0.1
). The latest
stable release is
1.1.0
.
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$
A CSV file describing sample contrasts
string
^\S+\.(csv|tsv|txt)$
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
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 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)?$
Path to directory or tar.gz archive for pre-built STAR index.
string
Path to directory or tar.gz archive for pre-built Salmon index.
string
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
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.
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
true
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
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
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
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 currently ‘star’.
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
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
Options related to riboseq-specific analysis modules
Extra arguments to pass to the ribotish quality command in addition to defaults defined by the pipeline.
string
Extra arguments to pass to the ribotish predict command in addition to defaults defined by the pipeline.
string
Extra arguments to pass to the ribotricer prepare-orfs command in addition to defaults defined by the pipeline.
string
Extra arguments to pass to the ribotricer detect-orfs command in addition to defaults defined by the pipeline.
string
Extra arguments to pass to anota2seq in addition to defaults defined by the pipeline.
string
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
true
Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.
boolean
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.
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 the adapter trimming step.
boolean
Skip all of the alignment-based processes within the pipeline.
boolean
Skip picard MarkDuplicates step.
boolean
Skip FastQC.
boolean
Skip MultiQC.
boolean
Skip all QC steps except for MultiQC.
boolean
Skip Ribo-TISH.
boolean
Skip Riboricer.
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
Base path / URL for data used in the test profiles
string
https://raw.githubusercontent.com/nf-core/test-datasets/riboseq/testdata/
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|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
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 hook 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
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean