modular version of the DNA protocol

[mvheetve]

Description of feature

Hi there,

As mentioned on Slack:#nanoseq https://nfcore.slack.com/archives/CP9GUPH35/p1690374727756149, I'm interested in running parts of the DNA protocol starting from a bam file. Nanoseq completion seemed succesful, but SNV variant calling was not executed, which is my main interest. No vcfs found in the work or output dir. All the pipeline seems to do is check the input and output a renamed copy of my alignment file.

Chris Hakkaart mentioned the RNA protocol was built to run modularly, but the DNA protocol is currently not. It would be a great improvement in terms of flexibility if the DNA protocol could be modified to a modular version. I'm currently not familiar with the code of this nf-core pipeline, but happy to assist in any way possible.

Here's the command I used for a first test run on a 60Gb bam file:

nextflow \
	run nf-core/nanoseq \
	--input ${samplesheet} \
	--outdir ${outputDir} \
	--protocol DNA \
	--skip_demultiplexing \
	--skip_alignment \
	--call_variants \
	--variant_caller medaka \
	--phase_vcf \
	--skip_sv \
	--skip_quantification \
	--skip_fusion_analysis \
	--skip_modification_analysis \
	-r 3.1.0 \
	-latest \
	-resume \
	-work-dir ${WORKDIR} \
	-profile vsc_ugent,$SLURM_CLUSTERS

Many thanks
Mattias