Make reference

Preprocess and build a transcriptome reference.

Info

ID: make_reference
Namespace: reference

Example input files are: - genome_fasta: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz - transcriptome_gtf: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz - ercc: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -main-script target/nextflow/reference/make_reference/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
genome_fasta: # please fill in - example: "genome_fasta.fa.gz"
transcriptome_gtf: # please fill in - example: "transcriptome.gtf.gz"
# ercc: "ercc.zip"
# subset_regex: "(ERCC-00002|chr1)"
# output_fasta: "$id.$key.output_fasta.gz"
# output_gtf: "$id.$key.output_gtf.gz"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/reference/make_reference/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name Description Attributes
--genome_fasta Reference genome fasta. Example: file, required, example: "genome_fasta.fa.gz"
--transcriptome_gtf Reference transcriptome annotation. file, required, example: "transcriptome.gtf.gz"
--ercc ERCC sequence and annotation file. file, example: "ercc.zip"
--subset_regex Will subset the reference chromosomes using the given regex. string, example: "(ERCC-00002|chr1)"
--output_fasta Output genome sequence fasta. file, required, example: "genome_sequence.fa.gz"
--output_gtf Output transcriptome annotation gtf. file, required, example: "transcriptome_annotation.gtf.gz"

Authors

  • Angela Oliveira Pisco (author)

  • Robrecht Cannoodt (author, maintainer)