filter-rnabloom2-transcripts

Filter RNABloom2 transcripts using Nexus

usage

nexus run --nf-workflow utilities_filter-rnabloom2-transcripts.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_filter "--min-mapping-quality 30 --min-read-support 3 --min-fraction-match 0.5"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘rnabloom2_output_dir’’.
--output_dir	Directory to which output files will be copied.
--params_filter	filter_rnabloom2_transcripts parameters (default: ‘“–min-mapping-quality 30 –min-read-support 3 –min-fraction-match 0.5”’). Note that the parameters need to be wrapped in quotes.