fix: Nextflow 25 strict syntax compliance for rnaseq modules and subworkflows

[pinin4fjords]

Summary

This PR fixes Nextflow 25 strict syntax compliance issues and converts modules to topics version output.

Strict Syntax Fixes:

Variable shadowing fixes:

• bbmap/bbsplit/main.nf: Rename closure variable index → idx to avoid shadowing input parameter

Implicit closure parameter it → explicit names:

• cat/fastq/main.nf: v, ix → val, idx
• gffread/main.nf: it → flag in .any { } closure
• rsem/preparereference/main.nf: it → arg in .removeIf { }
• salmon/quant/main.nf: it → r in .each { }
• sentieon/rsempreparereference/main.nf: it → arg in .removeIf { }
• sentieon/staralign/main.nf: it → r in .each { }
• trimgalore/main.nf: implicit it fix
• Multiple subworkflows: Fix implicit it in .map { }, .join { }, .branch { } operations

Sentieon env block fixes (5 test configs):

• Replace env { VAR = "$VAR" } syntax with env.VAR = System.getenv('VAR') syntax

Sentieon license variable usage:

• sentieon/rsemcalculateexpression/main.nf: Add $sentieonLicense to script (was defined but never used)
• sentieon/staralign/main.nf: Add $sentieonLicense to script (was defined but never used)

Unused variable removal in stubs:

• Various modules: Remove unused variable definitions in stub blocks

Topics Version Output Conversion (16 modules):

Converted from path "versions.yml", emit: versions to tuple val("${task.process}"), val('tool'), eval('version_cmd'), topic: versions, emit: versions_tool:

• bbmap/bbsplit
• bracken/bracken
• custom/catadditionalfasta
• gffread
• gunzip
• hisat2/extractsplicesites
• kraken2/kraken2
• rsem/preparereference
• salmon/quant
• sentieon/rsemcalculateexpression
• sentieon/rsempreparereference
• sentieon/staralign
• sortmerna
• sylph/profile
• ucsc/bedclip
• ucsc/bedgraphtobigwig

Subworkflows fixed (14 files):

• bam_dedup_stats_samtools_umicollapse
• bam_dedup_stats_samtools_umitools
• bam_dedup_umi
• bam_markduplicates_picard
• bam_sort_stats_samtools
• bam_stats_samtools
• bedgraph_bedclip_bedgraphtobigwig
• fastq_align_hisat2
• fastq_fastqc_umitools_fastp
• fastq_fastqc_umitools_trimgalore
• fastq_qc_trim_filter_setstrandedness
• fastq_remove_rrna
• fastq_subsample_fq_salmon
• quantify_pseudo_alignment

These changes ensure compliance with Nextflow 25 strict syntax.

Snapshot Updates (unrelated to strict syntax):

Some test snapshots were updated due to minor output changes in tools - these tests likely haven't run in a while and the snapshots were stale:

• antismash/antismash: Updated antismash.js md5 hash
• emboss/seqret: Updated test.gff md5 hash
• kofamscan: Updated test.kofamscan.txt md5 hash
• ultra/pipeline: Added new sorted field to JSON output

Additional Fixes:

• custom/catadditionalfasta: Fixed missing versions.yml creation in Python template after topics revert
• sentieon/rsemcalculateexpression & sentieon/rsempreparereference: Added STAR symlink to stub blocks to enable version detection
• Various subworkflows: Removed .out.versions references for modules converted to topics, and removed empty version channels where applicable

Test plan

• Run nextflow lint on modified files (verified locally - all pass)
• Run CI tests for affected modules
• Run CI tests for affected subworkflows

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