Code

Implement alignment subworkflow#6

Code

Merged

scwatts merged 87 commits intodevnf-core/oncoanalyser:devfrom alignment-subworkflownf-core/oncoanalyser:alignment-subworkflowCopy head branch name to clipboardApr 24, 2024

+2,234-461

Commits

Commits on Dec 1, 2023

• Basic isolated alignment subworkflow outline

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Commits on Feb 11, 2024

• Initial implementation of alignment workflow.

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• Simplified condition on whether fastp is run in alignment subworkflow.

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Commits on Feb 12, 2024

• Get rid of blocking when merging individual sample records back into a single group record.

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• Simple improvement to the alignment subworkflow.

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Commits on Feb 13, 2024

• Merge alignment and markdups logic into Stephen's stubs.

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• Updgrading from bwa mem to bwa mem2.

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• Fixing read group flag for bwa mem2.

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• Reassigning TODO.

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• Emiting versions.

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• Updating TODOs.

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• Fixing tags for new processes.

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  8ce78ff

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• Setting up targeted and wgts workflows for testing.

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Commits on Feb 14, 2024

• Minor fixes and style improvements.

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Commits on Feb 15, 2024

• Adding a TODO.

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Commits on Feb 18, 2024

• Add has_umis switch to markdups.

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• Force symlink overwrite so process does not fail on resume.

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• Change name of output bam from markdups.

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Commits on Feb 19, 2024

• Fix read group arg to bwa mem2.

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• Add TODO.

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• Fix markdups umi flags for TSO500 panel samples.

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• Add TODO.

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• Fix read group extraction from fastq filenames and a bug in the markdups stub.

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• Running with umis for targeted and without for wgts.

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• Fix includes in targeted.nf.

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• Only run markdups with UMIs when tso500 panel is selected.

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• Create switch between bwa mem and bwa mem2 for debugging purposes.

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Commits on Feb 20, 2024

• Add TODO.

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• Move new params into nextflow.config.

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• Add label to markdups process.

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Commits on Feb 21, 2024

• Disable all filtering and poly-g trimming in fastp.

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• Use fastp by default.

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• Remove bwa mem process.

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• Remove obsolete TODOs.

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• Pass ref genome version to markdups.

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• Add TODO.

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Commits on Feb 22, 2024

• Get versions from CLIs.

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• Delete Dockerfiles and update containers to biocontainer equivalents.

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  2c298c4

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• Removing temp config.

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• Fix process tags.

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  8d82bac

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• Reassign TODO.

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• Add TODO.

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Commits on Feb 23, 2024

• Align read group construction with HMF pipeline5.

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• Bump MarkDups to 1.1.1

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Commits on Feb 28, 2024

• Patch

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• Fix join for alignment BAM and corresponding BAIs

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• Improve comments, syntax, etc

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Commits on Feb 29, 2024

• Implement RNA alignment

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• Move, rename bwa-mem2 module

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• Fix bwa-mem2 process name

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• Set STAR process label to 'process_high'

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• Fix incomplete container URL for SAMtools sort

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• Handle when read count less than max read split

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• Correctly format RG arg for STAR

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• Fix bwa-mem2 bi-index variable name typo

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• Adjust, fix bwa-mem2 index handling

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• Remove deprecated MarkDups -multi_bam argument

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• Fix AMBER subworkflow TN mode

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• Fix COBALT subworkflow TN mode

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• Adjust indentation

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• Fix SAGE calling subworkflow TN mode

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• Improving handling of 'no merge' RNA BAM scenarios

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• Set outputs for alignment workflows

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• Add missing channel docs

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• Further work on RNA BAM handling

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• Use explicit returns in .branch ops

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• Do not index RNA BAMs prior to merge

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Commits on Mar 5, 2024

• Remove obsolete TODOs

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Commits on Mar 7, 2024

• Fix Isofox singularity container URL

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• Bump TSO500 data bundle version

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• Remove -force_pathogenic_pass in PAVE somatic

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Commits on Mar 16, 2024

• Correct prepare reference panel data path lookup

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• Merge branch 'dev' into alignment-subworkflow

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• Fix optional channel placeholders

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• Update modules.json

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• Adjust indenting

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Commits on Mar 18, 2024

• Use standard container directive format for STAR

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• Add missing imports and subworkflow descriptions

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Commits on Mar 19, 2024

• Use Bioconda/BioContainers for bwa-mem2 module

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Commits on Mar 27, 2024

• Improve naming for bwa-mem2 output BAMs

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Commits on Apr 15, 2024

• Use BAM index created during alignment

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Commits on Apr 22, 2024

• Improve BAM index selection

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• Include BAI in bwa-mem2/align stub

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• Adjust input selection logic

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Commits on Apr 23, 2024

• Bump MarkDups to 1.1.5

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• Remove Sambamba index module file

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• Add new meta.yaml

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