--skip_fastqc is not usable

[d4straub]

Description of the bug

Usage of --skip_fastqc crashes the pipeline.

Steps to reproduce

Steps to reproduce the behaviour:

nextflow run nf-core/ampliseq -r 2.1.0 -profile test,singularity --skip_fastqc

Error:

No such variable: info

 -- Check script 'ampliseq/./workflows/../subworkflows/local/parse_input.nf' at line: 61 or see '.nextflow.log' file for more details
Access to 'FASTQC.out' is undefined since process doesn't declare any output

 -- Check script 'ampliseq/./workflows/ampliseq.nf' at line: 584 or see '.nextflow.log' file for more details

Expected behaviour

No error.

Additional context

That line needs to read:

if (!params.skip_fastqc) {
    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
}

Also, the test profiles should probably use various skipping options to make sure those work!

[d4straub]

That's fixed in the dev branch.