workflows/ingestion/make_reference

Description

Build a transcriptomics reference into one of many formats.

Type

nextflow_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
star_genome_sa_index_nbases: [ 14 ]  
bdrhap_mitochondrial_contigs: [ "chrM", "chrMT", "M", "MT" ]  
target: [ "star" ]  
output_fasta: "$id.$key.output_fasta.gz"  
output_gtf: "$id.$key.output_gtf.gz"  
output_cellranger: "$id.$key.output_cellranger.gz"  
output_cellranger_arc: "$id.$key.output_cellranger_arc.gz"  
output_bd_rhapsody: "$id.$key.output_bd_rhapsody.gz"  
output_star: "$id.$key.output_star.gz"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/workflows/ingestion/make_reference/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the reference.
--genome_fasta	file required	Reference genome fasta.
--transcriptome_gtf	file required	Reference transcriptome annotation.
--ercc	file	ERCC sequence and annotation file.

Name

Type & Properties

--id

string

required

--genome_fasta

file

required

--transcriptome_gtf

file

required

--ercc

file

STAR Settings

Name	Type & Properties	Description
--star_genome_sa_index_nbases	integer	Length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter {genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1).

Name

Type & Properties

--star_genome_sa_index_nbases

integer

BD Rhapsody Settings

Name	Type & Properties	Description
--bdrhap_mitochondrial_contigs	string multiple	Names of the Mitochondrial contigs in the provided Reference Genome. Fragments originating from contigs other than these are identified as 'nuclear fragments' in the ATACseq analysis pipeline.
--bdrhap_filtering_off	boolean_true	By default the input Transcript Annotation files are filtered based on the gene_type/gene_biotype attribute. Only features having the following attribute values are kept: - protein_coding - lncRNA - IG_LV_gene - IG_V_gene - IG_V_pseudogene - IG_D_gene - IG_J_gene - IG_J_pseudogene - IG_C_gene - IG_C_pseudogene - TR_V_gene - TR_V_pseudogene - TR_D_gene - TR_J_gene - TR_J_pseudogene - TR_C_gene If you have already pre-filtered the input Annotation files and/or wish to turn-off the filtering, please set this option to True.
--bdrhap_wta_only_index	boolean_true	Build a WTA only index, otherwise builds a WTA + ATAC index.
--bdrhap_extra_star_params	string	Additional parameters to pass to STAR when building the genome index. Specify exactly like how you would on the command line.

Name

Type & Properties

--bdrhap_mitochondrial_contigs

string

multiple

--bdrhap_filtering_off

boolean_true

--bdrhap_wta_only_index

boolean_true

--bdrhap_extra_star_params

string

Cellranger ARC options

Name	Type & Properties	Description
--motifs_file	file	Path to file containing transcription factor motifs in JASPAR format.
--non_nuclear_contigs	string multiple	Name(s) of contig(s) that do not have any chromatin structure, for example, mitochondria or plastids. These contigs are excluded from peak calling since the entire contig will be "open" due to a lack of chromatin structure. Leave empty if there are no such contigs.

Name

Type & Properties

--motifs_file

file

--non_nuclear_contigs

string

multiple

Outputs

Name	Type & Properties	Description
--target	string multiple	Which reference indices to generate.
--output_fasta	file output	Output genome sequence fasta.
--output_gtf	file output	Output transcriptome annotation gtf.
--output_cellranger	file output	Output index
--output_cellranger_arc	file output	Output index
--output_bd_rhapsody	file output	Output index
--output_star	file output	Output index

Name

Type & Properties

--target

string

multiple

--output_fasta

file

output

--output_gtf

file

output

--output_cellranger

file

output

--output_cellranger_arc

file

output

--output_bd_rhapsody

file

output

--output_star

file

output

Arguments

Name	Type & Properties	Description
--subset_regex	string	Will subset the reference chromosomes using the given regex.

Name

Type & Properties

--subset_regex

string