wf-transcriptomes-v202/docs/06_inputs.md

Input Options

Nextflow parameter name	Type	Description	Help	Default
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.
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
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.
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.
ref_annotation	string	A reference annotation in GFF2 or GFF3 format (extensions .gtf(.gz), .gff(.gz), .gff3(.gz)). Only annotation files from Encode, Ensembl and NCBI are supported.	This will be used for guiding the transcriptome assembly and to label transcripts with their corresponding gene identifiers.
direct_rna	boolean	Set to true for direct RNA sequencing.	Omits the pychopper step.	False
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

Sample Options

Nextflow parameter name	Type	Description	Help	Default
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.
sample	string	A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of .fastq(.gz) files.

Options for reference-based workflow

Nextflow parameter name	Type	Description	Help	Default
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
gffcompare_opts	string	Extra command-line options to give to gffcompare -r	For a list of possible options see gffcompare.	-R
minimap2_index_opts	string	Extra command-line options for minimap2 indexing.	See minimap2 index options for more information. These will only be relevant in the reference based transcriptome assembly.	-k14
minimap2_opts	string	Additional command-line options for minimap2 alignment.	See minimap2 options for further information. These will only be relevant in the reference based transcriptome assembly.	-uf
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
stringtie_opts	string	Extra command-line options for stringtie transcript assembly.	For additional String tie options see here.	--conservative

Gene Fusion Detection Options

Nextflow parameter name	Type	Description	Help	Default
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.
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
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

Differential Expression Options

Nextflow parameter name	Type	Description	Help	Default
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
min_gene_expr	integer	Minimum gene counts	The minimum number of total mapped sequence reads for a gene to be considered expressed.	10
min_feature_expr	integer	Minimum transcript counts	The minimum number of total mapped sequence reads for a transcript to be considered.	3
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
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

Advanced Options

Nextflow parameter name	Type	Description	Help	Default
threads	integer	Number of CPU threads.	Only provided to processes including alignment and and assembly that benefit from multiple threads.	4
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
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
pychopper_opts	string	Extra pychopper opts	See available options (here)[https://github.com/epi2me-labs/pychopper#usage]
bundle_min_reads	integer	Minimum size of bam bundle for parallel processing.		50000
isoform_table_nrows	integer	Maximum rows to dispay in the isoform report table		5000

Miscellaneous Options

Nextflow parameter name	Type	Description	Help	Default
disable_ping	boolean	Enable to prevent sending a workflow ping.		False