fix: Nextflow profile

[tpall]

Description

• Fixed bug where Nextflow -profile option was inserted also second time with double hyphens (--profile ..) to nextflow call.
• Added snakemake extra parameter to pass other single hyphen options to nextflow (e.g. -resume []).
• Removed nextflow version from environment file.

All these have been tested by running nf-core/mag pipeline.

QC

For all wrappers added by this PR, I made sure that

• there is a test case which covers any introduced changes,
• input: and output: file paths in the resulting rule can be changed arbitrarily,
• either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
• rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
• all environment.yaml specifications follow the respective best practices,
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
• all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
• stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
• the meta.yaml contains a link to the documentation of the respective tool or command,
• Snakefiles pass the linting (snakemake --lint),
• Snakefiles are formatted with snakefmt,
• Python wrapper scripts are formatted with black.

[johanneskoester]

Can you please reformat your changes with black?

[fgvieira]

Are you using the latest black version? According to #460, GitHub Runners use version 22.1.0.

[johanneskoester]

You also need to format other wrappers (maybe just bad luck, sorry):

black bio/gatk/applybqsrspark/wrapper.py bio/biobambam2/bamsormadup/wrapper.py

[fgvieira]

Those formatting issues have already been fixed in master, so just rebase your branch to the current master.

[johanneskoester]

ping @tpall

[tpall]

I was using black version 21.6b0, but version 22.1.0 was happy too.

[johanneskoester]

Thanks!