DSL2: Update modules to use version topics

[TCLamnidis]

We need to update nf-core modules for tools user in nf-core/eager to include a versions topic.

Some of the modules listed below just need updating using nf-core modules update. Those can be ticked off.

Checklist:

• CAT_CAT
• CAT_FASTQ
• TABIX_BGZIP
• PICARD_CREATESEQUENCEDICTIONARY
• PICARD_MARKDUPLICATES
• SEQUENCETOOLS_PILEUPCALLER
• QUALIMAP_BAMQC
• AMPS
• MAPAD_MAP
• MAPAD_INDEX
• MULTIQC
• PMDTOOLS_FILTER
• BOWTIE2_ALIGN
• BOWTIE2_BUILD
• UNTAR
• MALT_RUN
• BAMUTIL_TRIMBAM
• MEGAN_RMA2INFO
• EIGENSTRATDATABASETOOLS_EIGENSTRATSNPCOVERAGE
• BCFTOOLS_INDEX
• BCFTOOLS_STATS
• PRINSEQPLUSPLUS
• ANGSD_DOCOUNTS
• ANGSD_GL
• ANGSD_CONTAMINATION
• DAMAGEPROFILER
• TAXPASTA_MERGE
• TAXPASTA_STANDARDISE
• MALTEXTRACT
• BWA_SAMPE- [ ] BWA_SAMSE
• BWA_INDEX
• BWA_MEM
• BWA_ALN
• SEXDETERRMINE
• MULTIVCFANALYZER
• PRESEQ_CCURVE
• PRESEQ_LCEXTRAP
• BEDTOOLS_MASKFASTA
• BEDTOOLS_COVERAGE
• FALCO
• GATK_UNIFIEDGENOTYPER
• GATK_INDELREALIGNER
• GATK_REALIGNERTARGETCREATOR
• MAPDAMAGE2
• KRAKEN2_KRAKEN2
• CIRCULARMAPPER_CIRCULARGENERATOR
• CIRCULARMAPPER_REALIGNSAMFILE
• MTNUCRATIO
• BBMAP_BBDUK
• FASTQC
• ENDORSPY
• SAMTOOLS_DEPTH
• SAMTOOLS_SORT
• SAMTOOLS_MERGE
• SAMTOOLS_MPILEUP
• SAMTOOLS_IDXSTATS
• SAMTOOLS_FAIDX
• SAMTOOLS_VIEW
• SAMTOOLS_INDEX
• SAMTOOLS_COLLATEFASTQ
• SAMTOOLS_FLAGSTAT
• SAMTOOLS_FASTQ
• ADAPTERREMOVAL
• METAPHLAN_METAPHLAN
• GATK4_HAPLOTYPECALLER
• SEQKIT_SPLIT2
• FREEBAYES
• FASTP
• KRAKENUNIQ_PRELOADEDKRAKENUNIQ
• DEDUP
• GUNZIP