nf-core/dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
22.10.6.
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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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringOption to generate mapping statistics, creating plots and summaries
booleanThis will create the following:
- Count the total number of reads before and after trimming
- Scatterplots comparing all replicates (separate for both host and pathogen reads)
- Plots of the % of mapped/quantified reads
- Plots of RNA-class statistics (as many types can be identified, the parameter below
--RNA_classes_to_replace_hostcan help to summarise these)
Reference igenome 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.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
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.
The path to the files should be enclosed by quotes "../.."
Change to custom name if desired, ie Human_hela_cells
stringChange to custom name if desired, ie Salmonella_SL1344
stringHost genome fasta file
stringPathogen genome fasta file
stringHost GFF file
stringPathogen GFF
stringHost transcriptome file
stringPathogen transcriptome file
stringBy default, the pipeline utilizes FastQC tool for quality control of sequencing reads, run before and after trimming
Define a set of additional fastqc parameters you wish to use, except --quiet --threads --noextract flags which are already specified in the dualrnaseq pipeline
stringAdapter and read trimming is performed by either Cutadapt or BBDuk.
Additional parameters if needed
stringDefine a set of additional Cutadapt parameters you wish to use, such as -a or -A to specify custom adapter sequences.
These parameters are available for Salmon in both Selective Alignment and Alignment-based mode
Options for setting the library type. A = automatic detection
stringThe pipeline uses gene features from the 3rd column of the host annotative file (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline useanscriptome_hosts exon from the --gff_host
string['exon', 'tRNA']The pipeline uses gene features from the 3rd column of the pathogen annotative fikle (gff3) to extract the coordinates of transcripts to be quantified. By default, the pipeline uses features as gene, sRNA, tRNA and rRNA from the --gff_pathogen file.
string['gene', 'sRNA', 'tRNA', 'rRNA']This flag defines the gene attribute from the 9th column of the host annotative (gff3) file, where the transcript names are extracted. By default, the pipeline extracts transcript_id from the --gff_host file
stringtranscript_idThis flag defines the gene attribute from the 9th column of the pathogen annotative (gff3) file, where transcript, genes or CDS regions are extracted. By default, the pipeline extracts locus_tag from the --gff_pathogen file
stringlocus_tagParameters listed below are available only for Salmon with Selective Alignment.
Run Salmon selective alignment. Does not need a value, just run --run_salmon_SA
booleantrueSet of additional parameters for creating an index with Salmon Selective Alignment. By default, the kmer size is set at 21. Multiple parameters can be passed - for example: --salmon_sa_index_args="--keepDuplicates -k 21".
string-k 21Set of additional parameters for mapping with Salmon Selective Alignment. By default, the pipeline allows soft-clipping of overhanging reads. Multiple parameters can be passed - for example: --salmon_sa_args="--softclipOverhangs --allowDovetail"
string--softclipOverhangsOptions for Alignment-based mode
To run Salmon alignment-based mode
booleanDefine a set of additional salmon quant parameters you wish to use in salmon alignment-based mode.
stringOptions for STAR genome alignment
To run STAR genome alignment
booleanOptions for HTSeq count
To run HTSeq count on a aligned genome file
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*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanDisable specified tools.
string^((baserecalibrator|baserecalibrator_report|bcftools|documentation|fastqc|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)?,?)*[^,]+$Multiple tools can be specified, separated by commas.