Updated a bunch of modules that failed nf-test because of the generation of compressed files using touch

[scorreard]

PR checklist

Closes #5409

Used the following command line to update all the main.nf : sed -i -r -e '/touch.*.gz/s/touch/echo "" | gzip >/' modules/nf-core/*/main.nf

[scorreard]

One of the tool doesn't have tests (getorganelle_fromreads), I openned an issue https://github.com/nf-core/modules/issues/8007 Solving this should solve 2 of the failing checks

[maxulysse]

pytests issues should be fixed when we migrate

[scorreard]

Creating issues associated to the failing tests :

• Getorganelle/fromreads failed chack: https://github.com/nf-core/modules/issues/8007
• strelka/somatic failed check : https://github.com/nf-core/modules/issues/8031
• phakorra failed check : https://github.com/nf-core/modules/issues/8032
• gatk4/mutect2 failed check : https://github.com/nf-core/modules/issues/8033

[famosab]

Removed getorganelle/fromreads

[famosab]

Remove change to gatk4/mergevcfs because that is used in a strelka related subworkflow #7969

[maxulysse]

Good catch up on this PR @famosab