Description
Preprocess and build a transcriptome 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
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output_fasta: "$id.$key.output_fasta.gz"
output_gtf: "$id.$key.output_gtf.gz"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision 1.0.3 \
-main-script target/nextflow/reference/make_reference/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--genome_fasta | file required |
--transcriptome_gtf | file required |
--ercc | file |
--subset_regex | string |
--output_fasta | file required output |
--output_gtf | file required output |