README.md

transcriptome_assembly_rnabloom2.nf

Assemble transcript sequences using long RNA reads using RNA-Bloom2.

Inputs / Outputs

I/O	Description
Input	fastq.gz file for each sample.
Output	RNA-Bloom2 output files including FASTA file for each sample.

Dependencies

• RNA-Bloom2

Example

nexus run --nf-workflow transcriptome_assembly_rnabloom2.nf \
    -c NEXTFLOW_CONFIG_FILE \
    -w WORK_DIR \
    --samples_tsv_file SAMPLES_TSV_FILE \
    --output_dir OUTPUT_DIR \
    --params_rnabloom2 '"--qual 20 --qual-avg 20 --mincov 3 -ntcard -savebf"'

Usage

workflow:
    1. Assemble transcripts using RNA-Bloom2.

usage: nexus run --nf-workflow transcriptome_assembly_rnabloom2.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:
    --params_rnabloom2                  :   RNA-Bloom2 parameters (default: '"--qual 20 --qual-avg 20 --mincov 3 -ntcard -savebf"').
                                            Note that the parameters need to be wrapped in quotes.
    --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

--params_rnabloom2

• Refer to the RNA-Bloom2 documentation.
• The following parameters for RNA-Bloom2 are already included in nexus module for RNA-Bloom2 and should not be specified:
  • -long
  • --threads
  • --outdir