Fix aws labels cost tracking issue

[edmundmiller]

AWS tag validation issues were addressed by sanitizing process tags across multiple Nextflow modules. The primary problem involved illegal characters in tag values, such as ^ in restriction sites or = in sample identifiers, which violate AWS resource label constraints.

A consistent sanitization pattern, replaceAll(/[^a-zA-Z0-9_-]/, '_'), was applied. This regex replaces any character not a letter, number, underscore, or hyphen with an underscore, ensuring AWS compliance.

Specific changes include:

• In modules/local/hicpro/get_restriction_fragments.nf, the res_site tag was sanitized (e.g., ^GATC becomes _GATC).
• In modules/local/hicpro/dnase_mapping_stats.nf, sample and bam tags were combined and sanitized (e.g., sample = file.bam becomes sample___file_bam).
• In modules/nf-core/bwa/index/main.nf, modules/nf-core/bowtie2/build/main.nf, and modules/nf-core/custom/getchromsizes/main.nf, fasta base names were sanitized (e.g., genome.fasta becomes genome_fasta).
• In modules/nf-core/cooler/makebins/main.nf, a syntax error "${meta.id}}" was corrected to "${meta.id}".

These modifications ensure all generated process tags adhere to AWS naming conventions, resolving potential deployment errors.

Closes #224

[ewels]

@edmundmiller this is an ancient PR, but you've modified shared modules here without updating them. Are these updated upstream? Can we do it that way then just pull in updates insatead?