[BUG]: Different processes between Illumina and Nanopore platforms

[kdl480]

Is there an existing issue for this?

• [X] I have searched the existing issues

Description of the Bug/Issue

I'm working on validating this pipeline on samples sequenced on both Illumina and Nanopore platforms. I noticed the processes are different between the two, with more results being provided with the Nanopore platform (e.g. coverage_plots, mapping, mosdepth, MultiQC, read_count, reference_sequences, variants). Is there any way to have these processes included with the Illumina workflow as well?

Nextflow command-line

nextflow run CFIA-NCFAD/nf-flu --input samplesheet.csv --platform nanopore/illumina -profile conda

Error Message

Missing these result directories with the Illumina work flow:
coverage_plots, mapping, mosdepth, MultiQC, read_count, reference_sequences, variants

Workflow Version

v3.1.0

Nextflow Executor

local

Nextflow Version

22.04.3

Java Version

openjdk 11.0.9.1-internal 2020-11-04 OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src) OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)

Hardware

Desktop

Operating System (OS)

Ubuntu 20.04

Conda/Container Engine

Conda

Additional context

No response

[peterk87]

Hi @kdl480 it's on the roadmap. We've transitioned to doing the majority of our influenza sequencing on Nanopore so getting the Nanopore workflow up and running with the features we needed was a top priority. The Illumina subworkflow will have the same steps added soon.

[kdl480]

Okay, sounds great. Thank you so much for these :)

[stefkary]

@peterk87 I was wondering if there are any updates on full Illumina implementation of the pipeline? We would be really interested to have the first table in the Multi-QC to be able to compare runs on Illumina and Nanopore more easily.