Simon Pearce

Ugh, this is bad, the consensus should definitely be being made in the merged lanes. I'd highly recommend using the [nf-core/fastquorum](https://github.com/nf-core/fastquorum/tree/master) pipeline for consensus read generation instead.

> What is the state of this docs update, @SPPearce ? @jfy133 and @nvnieuwk are still against it as far as I know, but I still don't understand why. The...

Huh, I thought this had actually been merged a while ago. Can we merge this now?

Not currently working as the test gives an error :(

Thanks @awgymer !

I do think that using a parameter instead of `workflow.containerEngine` is the neater solution, in case there are further options in the future it wouldn't require changing all the modules...

Matthias, do you know of any modules that aren't hard coded with singularity? A bulk update to that line would be straightforward enough, while we have bulk updates to do...

Yes, it doesn't seem to have ever been actioned on. As you say, the Seqera containers tools support doesn't seem to actually be being pushed at all..., but when it...

``` ./modules/nf-core/adapterremoval/tests/main.nf.test ./modules/nf-core/ampcombi/tests/main.nf.test ./modules/nf-core/ampcombi2/cluster/tests/main.nf.test ./modules/nf-core/ampcombi2/complete/tests/main.nf.test ./modules/nf-core/ampcombi2/parsetables/tests/main.nf.test ./modules/nf-core/antismash/antismashlite/tests/main.nf.test ./modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test ./modules/nf-core/bases2fastq/tests/main.nf.test ./modules/nf-core/bcl2fastq/tests/main.nf.test ./modules/nf-core/bclconvert/tests/main.nf.test ./modules/nf-core/cat/fastq/tests/main.nf.test ./modules/nf-core/centrifuge/centrifuge/tests/main.nf.test ./modules/nf-core/centrifuge/kreport/tests/main.nf.test ./modules/nf-core/checkv/endtoend/tests/main.nf.test ./modules/nf-core/checkv/updatedatabase/tests/main.nf.test ./modules/nf-core/csvtk/concat/tests/main.nf.test ./modules/nf-core/csvtk/join/tests/main.nf.test ./modules/nf-core/dragmap/hashtable/tests/main.nf.test ./modules/nf-core/dragonflye/tests/main.nf.test ./modules/nf-core/eggnogmapper/tests/main.nf.test ./modules/nf-core/fastme/tests/main.nf.test ./modules/nf-core/fastqc/tests/main.nf.test ./modules/nf-core/flye/tests/main.nf.test ./modules/nf-core/gatk4/svcluster/tests/main.nf.test ./modules/nf-core/glimpse2/chunk/tests/main.nf.test ./modules/nf-core/hamronization/amrfinderplus/tests/main.nf.test ./modules/nf-core/hmmer/hmmsearch/tests/main.nf.test ./modules/nf-core/igvreports/tests/main.nf.test ./modules/nf-core/iqtree/tests/main.nf.test...

Well, we have something like 110 pipelines in total including the archived ones, so that doesn't sound too bad