multiqc module improvements

[samleenz]

• allow naming of report using the $params.project variable -n ${params.project}
• improve file naming, make input a tuple (name dir)?
• extend to parse other outputs (salmon / star / featureCounts etc)

need to sort how to deal with optional arguments with nextflow processes

[samleenz]

For point three, one option I am testing is just combine all output channels of interesting before passing to multiqc as a channel containing a single list

for example:

    multiqc_ch = RUN_MULTIQC(
        fastqc_ch
            .concat(star_logs_pass2_ch)
            .collect()
        )

[samleenz]

above appears to work well. Will just be good to sort out the naming of samples within multiqc. may require a specific multiQC config file?