Add the consensus_bcftools subworkflow prototype

[sgsutcliffe]

We, the Montreal team, mocked up a subworkflow for the issue 127, we added the additional missing modules that we needed from viralrecon.

We took one local module from viralrecon (RENAME_FASTA_HEADER) and converted one nf-core module to localBEDTOOLS_GENOMECOV to use a new param.genomecov_threshold with a default as 10 (as was in the line here)

bedtools genomecov -bga -ibam $BAM | awk '$4 < 10' > low_coverage_sites.bed

Note: BEDTOOLS_GENOMECOV is pending a nf-core invite request from a team-member.

[avantonder]

Please add a resource label : label 'process_single'

[sgsutcliffe]

c0ad3d1

[avantonder]

Please can you change the channel names to match the template usually used by nf-core e.g. ch_query instead of query_channel.

Please remove commented out gff and nextclade_db inputs

[sgsutcliffe]

760a87c

[avantonder]

Thanks, this looks great. Please can you address the changes and I will merge the PR once this is done and bedtools genomecov has been added.

[sgsutcliffe]

Thanks for the comments! The bedtools genomecov tool is in PR#141 and the comments have been addressed.