parabricks/fq2bam version updated and tests migrated to nftest

[bojangles2002]

PR checklist

Closes #6860

• [ X ] This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• [ X ] Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[famosab]

We might need to update these declarations (at least I got some errors):
def metrics_output_command = args = "--out-duplicate-metrics duplicate-metrics.txt" ? "touch duplicate-metrics.txt" : "" def known_sites_output_command = known_sites ? "touch ${prefix}.table" : "" def qc_metrics_output_command = args = "--out-qc-metrics-dir qc_metrics " ? "mkdir qc_metrics && touch qc_metrics/alignment.txt" : ""
to

    def metrics_output_command = args.contains("--out-duplicate-metrics duplicate-metrics.txt") ? "touch duplicate-metrics.txt" : ""
    def known_sites_output_command = known_sites ? "touch ${prefix}.table" : ""
    def qc_metrics_output_command = args.contains("--out-qc-metrics-dir qc_metrics ") ? "mkdir qc_metrics && touch qc_metrics/alignment.txt" : ""

[famosab]

this is just a note if we run into errors later

[famosab]

be careful: i think the meta should not be changed, it seems that this now adheres to. an older structure

[famosab]

Suggested change

	test("parabricks_fq2bam_pe_default") {
	test("sarscov2 - fastq.gz - paired-end") {

[famosab]

Suggested change

	test("parabricks_fq2bam_se_default") {
	test("sarscov2 - fastq.gz - single-end") {

[famosab]

Suggested change

	test("parabricks_fq2bam_se_default_stub") {
	test("sarscov2 - fastq.gz - single-end - stub") {

[famosab]

this came from the pytest, right? I do not think we really need this anymore but we need to take care that all of this is reflected in the new nf-test

[famosab]

solved with #6902