Pre-release issue fixes

[drpatelh]

Closes #664
Closes #720
Closes #725
Closes #727

[mahesh-panchal]

Line 193 in modules.config also needs:

if (!(params.skip_fastqc || params.skip_qc)) {
    process {
        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
            ext.args   = '--quiet'
        }
    }
}

It's appearing in tests that are passing. https://github.com/nf-core/rnaseq/runs/4510962412?check_suite_focus=true

[mahesh-panchal]

Also need the conditional for '.*:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE'

if (!params.skip_trimming){
    process {
        withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
        ...

[mahesh-panchal]

WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*
WARN: There's no process matching config selector: .*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC

with Test Salmon with workflow parameters (--skip_qc --skip_alignment)

The NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.* selector may need to be split up into it's respective block.
e.g.
NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*

[drpatelh]

Forgot we are running all of these tests! Be great if you can create a separate in PR fixing up those WARN . I will go through them again after you are done. Think we need to add some more comments to modules.config to break things up a little because it's quite easy to get lost in all of the buried config.