long_read_rna_alignment_ultra

long_read_rna_alignment_ultra.nf

Aligns long RNA reads (Pacific Biosciences or Oxford Nanopore) to a reference genome using uLTRA.

Inputs / Outputs

I/O	Description
Input	fastq.gz file for each sample.
Output	MD-tagged and sorted bam and bam.bai files for each sample.

Dependencies

• uLTRA
• samtools

Example

nexus run --nf-workflow long_read_rna_alignment_ultra.nf \
    -c NEXTFLOW_CONFIG_FILE \
    -w WORK_DIR \
    --samples_tsv_file SAMPLES_TSV_FILE \
    --output_dir OUTPUT_DIR \
    --reference_genome_fasta_file REFERENCE_GENOME_FASTA_FILE \
    --reference_genome_fasta_fai_file REFERENCE_GENOME_FASTA_FAI_FILE \
    --ultra_index ULTRA_INDEX \
    --params_ultra '"--isoseq"'

Usage

workflow:
    1. Align reads (fastq.gz files) to a reference genome using uLTRA.
    2. Generate MD tags.
    3. Sort MD-tagged bam file.

usage: nexus run --nf-workflow long_read_rna_alignment_ultra.nf [required] [optional] [--help]

required arguments:
    -c                                  :   Nextflow .config file.
    -w                                  :   Nextflow work directory path.
    --samples_tsv_file                  :   TSV file with the following columns:
                                            'sample_id', 'fastq_file'.
    --output_dir                        :   Directory to which output files will be copied.

optional arguments:
    --reference_genome_fasta_file       :   Reference genome FASTA file (default: /datastore/lbcfs/collaborations/pirl/seqdata/references/hg38.fa).
    --reference_genome_fasta_fai_file   :   Reference genome FASTA.FAI file (default: /datastore/lbcfs/collaborations/pirl/seqdata/references/hg38.fa.fai).
    --ultra_index                       :   uLTRA index path (default: /datastore/lbcfs/collaborations/pirl/seqdata/tool-resources/ultra/hg38_index/).
    --params_ultra                      :   uLTRA parameters (default: "--isoseq").
    --delete_work_dir                   :   Delete work directory (default: false).

Parameters

-c

• Nextflow config file can be downloaded here

--samples_tsv_file

• A TSV (tab-separated values) file with the following headers:

Header	Description
sample_id	Sample ID.
fastq_file	Full path to fastq.gz file

--reference_genome_fasta_file

• Reference genome FASTA files can be found in /datastore/lbcfs/collaborations/pirl/seqdata/references/ on LBG.

--ultra_index

• An uLTRA index needs to be generated prior to running this workflow.
• Prebuilt uLTRA indices are available in /datastore/lbcfs/collaborations/pirl/seqdata/tool-resources/ultra/ on LBG.

--params_ultra

• Refer to the uLTRA documentation.
• The following parameters for minimap2 are already included in nexus module for minimap2 and should not be specified:
  • --t
  • --index
  • --prefix