fix: gs10 data partition; container syntax; input file name collision in Octopus; AnnotSV missing db; name tag

[samarth8392]

Changes

This PR address various issues:

1. Removed /gs10 data partition from ci_stub.config and nextflow.config

fixes #110

2. Changed continer syntax

• container = "${params.containers}" to container "${params.containers}" for all local modules
• The old syntax was setting the container as NULL leading to errors like fastp command not found

3. Fix input file name collision in Octopus variant calling

Nextflow was failing with input file name collision errors when running Octopus variant caller:

Process `VC_TONLY:combineVariants_alternative` input file name collision -- 
There are multiple input files for each of the following file names: 
*.tonly.octopus.vcf.gz, *.tonly.octopus.vcf.gz.tbi

The bambyinterval channel was being reused across multiple variant calling processes (mutect2, vardict, varscan, octopus). This caused duplicate interval files to be processed and collected by groupTuple(), resulting in the same VCF file appearing multiple times in the input lists.

Added .unique() deduplication after sorting VCF and index files in the Octopus workflow sections:

• workflows/tumoronly.nf: Added .unique() to Octopus tumor-only workflow
• workflows/tumornormal.nf: Added .unique() to Octopus paired (TN) and tumor-only workflows

4. Fix AnnotSV database path resolution in tumor-only SV workflows

AnnotSV was failing due to incorrect or inconsistent database path configuration (-annotationsDir) in SV workflows. The process did not provide a annotsv_db path, which led to default path from within the container which did not exist inside the container, causing AnnotSV to fail during configuration loading.

This PR standardizes and externalizes the AnnotSV database configuration using genome-specific parameters.

5. Fix undefined tag variable in bwamem2 process

The bwamem2 process was using an undefined variable name in the tag directive, which would cause the tag to be empty or throw an error.
Process input parameter is named samplename, but the tag directive was referencing name

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
• [] Update docs if there are any API changes.
• [ ] If a new nextflow process is implemented, define the process container and stub.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kelly-sovacool]

I went ahead and added a few lines to the changelog. Thanks for fixing these bugs Samarth!