nf-core/smrnaseq
A small-RNA sequencing analysis pipeline
2.0.0). The latest
stable release is
2.4.0
.
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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Protocol for constructing smRNA-seq libraries.
stringPresets for trimming parameters and 3' adapter sequence with a specified protocol.
| Protocol | Library Prep Kit | Trimming Parameter | 3' Adapter Sequence |
| :------------ | :-------------------------------------- | :-------------------------------------- | :--------------------- |
| illumina | Illumina TruSeq Small RNA | clip_r1 = 0 three_prime_clip_r1 = 0 | TGGAATTCTCGGGTGCCAAGG |
| nextflex | BIOO SCIENTIFIC NEXTFLEX Small RNA-Seq | clip_r1 = 4 three_prime_clip_r1 = 4 | TGGAATTCTCGGGTGCCAAGG |
| qiaseq | QIAGEN QIAseq miRNA | clip_r1 = 0 three_prime_clip_r1 = 0 | AACTGTAGGCACCATCAAT |
| cats | Diagenode CATS Small RNA-seq | clip_r1 = 3 three_prime_clip_r1 = 0 | AAAAAAAAAAA + GATCGGAAGAGCACACGTCTG (only polyA is used for trimming) |
| custom | user defined | user defined | user defined |
NB: When running
--protocol customthe user must define the 3' Adapter Sequence.
If trimming parameters aren't provided the pipeline will deafult toclip_R1 = 0andthree_prime_clip_R1 = 0(i.e. no extra clipping).
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
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.
Species for miRTrace.
stringThis is automatically set when using --genome. Example values: hsa, mmu...
Note that mirTrace relies on miRBase for its species reference. See available references here.
Path to reference genome FASTA genome file.
stringIf you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.
GFF/GTF file with coordinates positions of precursor and miRNAs.
stringmiRBase .gff3 file, typically downloaded from https://mirbase.org/ftp/CURRENT/genomes/
If using iGenomes with --genome this file will be downloaded from miRBase automatically during the pipeline run.
Path to FASTA file with mature miRNAs.
stringhttps://mirbase.org/ftp/CURRENT/mature.fa.gzTypically this will be the mature.fa file from miRBase. Can be given either as a plain text .fa file or a compressed .gz file.
Defaults to the current miRBase release URL, from which the file will be downloaded.
Path to FASTA file with miRNAs precursors.
stringhttps://mirbase.org/ftp/CURRENT/hairpin.fa.gzTypically this will be the mature.fa file from miRBase. Can be given either as a plain text .fa file or a compressed .gz file.
Defaults to the current miRBase release URL, from which the file will be downloaded.
Path to a Bowtie 1 index directory
stringPoint to the directory created by Bowtie 1 when indexing. Bowtie 1 indices consist of six files:
genome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt
Save generated reference genome files to results.
booleanSaving generated references means that you can use them for future pipeline runs, reducing processing times.
Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo 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.
Options for trimming reads and primers.
Discard reads that are shorter than this after quality / adapter trimming.
integer17The number of basepairs to remove from the 5' end of read 1.
integerThe number of basepairs to remove from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
integerSequencing adapter sequence to use for trimming.
stringTGGAATTCTCGGGTGCCAAGGThe miRTrace protocol for QC reporting.
stringmiRTrace can handle four protocols, each with their own primer-read structure. See the protocol descriptions here.
The max-length parameter used for trimming with TrimGalore!.
integer40Switches to skip specific pipeline steps, if desired.
Skip all QC steps
booleanSkip FastQC
booleanSkip miRDeep
booleanSkip MultiQC
booleanSkip all trimming steps.
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/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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
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.
booleanCustom config file to supply to MultiQC.
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
booleanRun this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.
boolean