Synchronization

:wave: Hey there, After our hackaton, @abhi18av and I discussed our main strategy for taking the Qc-subworkflow forward.

I'm trying to synchronize dev branch with qc-subworkflow to explain the overall content of several (72) iterations over the code.

My main observation is: There are inconsistencies on the process expected output vs the generated, and commonly we have null.extension on the resolved output, which lead to a successful code execution and process fail due missing output file.

I had to give some attention to the python scripts also, and the usage of templates that we need remove in prior of using only binaries.

Finally, I've a question regarding decision making code.

if ( params.sexinfo_available =! true) {
            sexinfo = "--allow-no-sex"
            extrasexinfo = ""
            //println "Sexinfo not available, command --allow-no-sex\n"
            } else {
            sexinfo = ""
            extrasexinfo = "--must-have-sex"
            //println "Sexinfo available command"
            }

On the original h3gwas pipeline, this logic is on the qc workflow and not inside the modules as the task of accessing sexinfo and extrasexinfo is recurrent. Should we follow the same process and turn sexInfo into a parameter to be accessed by each module? or we should use as configuration to be used as external parameter by the module? following nf-core structure?

I'd like to request help on the COMP_PCA process, as I can't understand why we're getting null.eigenval on the output, everything seems to be right to me.

Thank you for you attention, let's keep this pace until v1 release :rocket:

Kindly, Davi

nf-core / gwas

Synchronization after several iterations #43

Synchronization