73 lines
8.2 KiB
Markdown
73 lines
8.2 KiB
Markdown
### Input Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| fastq | string | FASTQ files to use in the analysis. | This accepts one of three cases: (i) the path to a single FASTQ file; (ii) the path to a top-level directory containing FASTQ files; (iii) the path to a directory containing one level of sub-directories which in turn contain FASTQ files. In the first and second case, a sample name can be supplied with `--sample`. In the last case, the data is assumed to be multiplexed with the names of the sub-directories as barcodes. In this case, a sample sheet can be provided with `--sample_sheet`. | |
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| transcriptome_source | string | Select how the transcriptome used for analysis should be prepared. | To analyse only gene fusions and differential expression use of an existing transcriptome may be preferred and so 'precomputed' should be selected. In this case the 'ref_transcriptome' parameter should be specified. To create a reference transcriptome using an existing reference genome, select 'reference guided' and specify the 'ref_genome' parameter. | reference-guided |
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| ref_genome | string | Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow. | A reference genome is required for reference-based assembly of a transcriptome. | |
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| ref_transcriptome | string | Transcriptome reference file. Required for precomputed transcriptome calculation and for differential expression analysis. | A reference transcriptome related to the sample under study. Must be supplied when the 'Transcriptome source' parameter has been set to 'precomputed' or to perform differential expression. | |
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| ref_annotation | string | A reference annotation in GFF2 or GFF3 format (extensions .gtf(.gz), .gff(.gz), .gff3(.gz)). Only annotation files from [Encode](https://www.encodeproject.org), [Ensembl](https://www.ensembl.org/index.html) and [NCBI](https://www.ncbi.nlm.nih.gov/) are supported. | This will be used for guiding the transcriptome assembly and to label transcripts with their corresponding gene identifiers. | |
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| direct_rna | boolean | Set to true for direct RNA sequencing. | Omits the pychopper step. | False |
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| analyse_unclassified | boolean | Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified directory. | If selected and if the input is a multiplex directory the workflow will also process the unclassified directory. | False |
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### Sample Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| sample_sheet | string | A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a directory containing sub-directories with FASTQ files. If you are running the differential expression workflow, there must be an additional column `condition` with two labels, one of which must be `control` (e.g. `control` and `treated`). Control will indicate which samples will be used as the reference. There should be at least 3 repeats for each condition. | The sample sheet is a CSV file with, minimally, columns named `barcode` and `alias`. Extra columns are allowed. | |
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| sample | string | A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of .fastq(.gz) files. | | |
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### Options for reference-based workflow
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| plot_gffcmp_stats | boolean | Create a PDF of plots from showing gffcompare results | If set to true, a PDF file containing detailed gffcompare reults will be output | True |
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| gffcompare_opts | string | Extra command-line options to give to gffcompare -r | For a list of possible options see [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml). | -R |
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| minimap2_index_opts | string | Extra command-line options for minimap2 indexing. | See [minimap2 index options](https://lh3.github.io/minimap2/minimap2.html#4) for more information. These will only be relevant in the reference based transcriptome assembly. | -k14 |
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| minimap2_opts | string | Additional command-line options for minimap2 alignment. | See [minimap2 options](https://lh3.github.io/minimap2/minimap2.html#5) for further information. These will only be relevant in the reference based transcriptome assembly. | -uf |
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| minimum_mapping_quality | integer | filter aligned reads by MAPQ quality. | Reads that do not meet this mapping quality after minimap2 alignment, will be filtered out. | 40 |
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| stringtie_opts | string | Extra command-line options for stringtie transcript assembly. | For additional String tie options see [here](https://github.com/gpertea/stringtie#stringtie-options). | --conservative |
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### Gene Fusion Detection Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| jaffal_refBase | string | JAFFAl reference genome directory. | JAFFAL human hg38 reference data directory can be downloaded from here: https://figshare.com/ndownloader/files/25410494 or see the README for alternative instructions. If custom gemome files are required, see the instructions here: https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#how-can-i-generate-the-reference-files-for-a-non-supported-genome. | |
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| jaffal_genome | string | Genome reference prefix. e.g. hg38. | JAFFAL reference files are prefixed with the genome reference file name and need to be supplied . If using the human reference data provided by JAFFAL, this can be left at `hg38`. | hg38 |
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| jaffal_annotation | string | Annotation suffix. | JAFFAL reference files are suffixed with the annotation filename and this needs to be supplied. For the human hg38 reference data supplied by JAFFAL, this is `genCode22`. | genCode22 |
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### Differential Expression Options
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| Nextflow parameter name | Type | Description | Help | Default |
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|--------------------------|------|-------------|------|---------|
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| de_analysis | boolean | Run DE anaylsis | Running this requires you to provide at least two replicates for a control and treated sample as well as a sample sheet param. | False |
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| min_gene_expr | integer | Minimum gene counts | The minimum number of total mapped sequence reads for a gene to be considered expressed. | 10 |
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| min_feature_expr | integer | Minimum transcript counts | The minimum number of total mapped sequence reads for a transcript to be considered. | 3 |
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| min_samps_gene_expr | integer | Genes expressed in a minimum of this many samples will be included in the differential expression analysis. | A gene must be mapped to at least this minimum number of samples for the gene be included in the analysis. | 3 |
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| min_samps_feature_expr | integer | Transcripts expressed in minimum this many samples | A transcript must be mapped in at least this this minimum number of samples to be included in the analysis. | 1 |
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### Advanced Options
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| Nextflow parameter name | Type | Description | Help | Default |
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| threads | integer | Number of CPU threads. | Only provided to processes including alignment and and assembly that benefit from multiple threads. | 4 |
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| cdna_kit | string | If cDNA reads are used, select the kit used. | This will be used by pychopper to preprocess the reads for downstream analysis. | SQK-PCS109 |
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| pychopper_backend | string | Pychopper can use one of two available backends for identifying primers in the raw reads | 'edlib' is set by default due to its high performance. However, it may be less sensitive than 'phmm'. | edlib |
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| pychopper_opts | string | Extra pychopper opts | See available options (here)[https://github.com/epi2me-labs/pychopper#usage] | |
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| bundle_min_reads | integer | Minimum size of bam bundle for parallel processing. | | 50000 |
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| isoform_table_nrows | integer | Maximum rows to dispay in the isoform report table | | 5000 |
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### Miscellaneous Options
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| Nextflow parameter name | Type | Description | Help | Default |
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| disable_ping | boolean | Enable to prevent sending a workflow ping. | | False |
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