Add KALLISTO module

[ctuni]

Currently kallisto is run as follows for index building and quantification. .fasta file is defined before. These processes need to be implemented as modules in the workflow.

else{
        process Build_kallisto_index_of_GTF_for_quantification {

            input:
            file transript_fasta from finalFasta_for_quantification_gtf

            output:
            file "transcripts.idx" into final_kallisto_index

            shell:
            '''
            #index kallisto reference 
            kallisto index -i transcripts.idx !{transript_fasta}
            
            '''
        }
        constant_kallisto_index = final_kallisto_index.first()
        process Run_kallisto_for_quantification {


            tag { file_tag }
            label 'para'

            input:
            file kallistoIndex from constant_kallisto_index
            set val(samplename), file(pair) from readPairs_for_kallisto

            output:
            file "${file_tag_new}_abundance.tsv" into kallisto_tcv_collection

            shell:
            file_tag = samplename
            file_tag_new = file_tag
            if (params.singleEnd) {
                println print_purple("Quantification by kallisto in single end mode")
                '''
                #quantification by kallisto in single end mode
                kallisto quant -i !{kallistoIndex} -o !{file_tag_new}_kallisto -t !{task.cpus} -b 100 --single -l 180 -s 20  !{pair} 
                mv !{file_tag_new}_kallisto/abundance.tsv !{file_tag_new}_abundance.tsv
                '''


            }

[opetryk]

@Emeerdink can you please provide a description to this task? What functionality of KALLISTO you would like to use in pipeline?

[opetryk]

@Emeerdink thank you for the description. As I see nf-core/lncpipe has only 2 modules fastqc and multiqc and both of that modules do not produce desired input for the kallisto modules. As I see from the code you shared, previous version of the pipeline was dsl1. Can you share the link to that old version to be able to see the business logic that needs to be applied in the pipeline?

[Emeerdink]

@opetryk https://github.com/nf-core/lncpipe/blob/dev_dsl1/main.nf This is the old version. We are trying to get started with transferring all that stuff into modules in the new pipeline