changing remotes for nf-core modules in reads_bwamem2_decontamination

[vagkaratzas]

I removed the two local modules since they are not used in any other subworkflow here.

A couple of things. The bwamem nf-core module declares 4 inputs instead of the local one which declared 2. Should the subworkflow take 4 now as well? Or should we give empty stuff in the nf-tests @Ales-ibt ?

Which takes me to my next observation. The test folder is >10MB, and we could potentially remove everything and use the test files from the respective nf-core modules:
Example bwamem2_mem test:

input[0] = Channel.of([
                    [ id:'test', single_end:true ], // meta map
                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)]
                ])
                input[1] = BWAMEM2_INDEX.out.index
                input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]])
                input[3] = false

Let me know your thought

[Ales-ibt]

Hello there! Nice you are revisiting this subwf. However, I think we are not using it anymore, I am not sure. Instead, we should be using the bwamem2decontnobams module, that write down the decontaminated reads on the fly without generating intermediate bam files

[vagkaratzas]

Hello there! Nice you are revisiting this subwf. However, I think we are not using it anymore, I am not sure. Instead, we should be using the bwamem2decontnobams module, that write down the decontaminated reads on the fly without generating intermediate bam files

raw-reads-analysis-pipeline is using it according to https://ebi-metagenomics.github.io/nf-modules/subworkflows/ebi-metagenomics/reads_bwamem2_decontamination/.
@timrozday-mgnify , I will need your input for this one. Are you still using it? Should you switch to bwamem2decontnobams which Ales suggested? Or would you prefer me updating the subworkflow here with 4 inputs as in nf-core?

[Ales-ibt]

It looks good, I think we can make the change to use the four inputs as in nf-core module and use their tests.

[Ales-ibt]

The other two inputs are:

    tuple val(meta3), path(fasta)  // This is the reference genome in fasta format 
    val   sort_bam                 // This is a boolean: use samtools sort (true) or samtools view (false)

Fasta is required for cram output, so as far as we don't use cram as extension for the output format arg, we could pass an empty tuple.

[timrozday-mgnify]

It looks like the module in raw-reads pipeline can be swapped for bwamem2decontnobams, however I just need to check that the samtools view flags are suitable.

[vagkaratzas]

It looks like the module in raw-reads pipeline can be swapped for bwamem2decontnobams, however I just need to check that the samtools view flags are suitable.

Let me know so I can completely remove this subworkflow from the repo, along with the modules

[timrozday-mgnify]

Yes it can be deleted, I will start a PR for modifying the sam flags in bwamem2decontnobams

[Ales-ibt]

Let's delete this module. Thanks @vagkaratzas

[Ales-ibt]

After discussion with @timrozday-mgnify, this module is going to be removed due to lack of use and the availability of an option that don't write bam files