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

  scwatts

  committed
  86220ec

Commits on Feb 11, 2024

• Initial implementation of alignment workflow.

  mkcmkc

  committed
  4e92135

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

  mkcmkc

  committed
  f69caf9

Commits on Feb 12, 2024

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

  mkcmkc

  committed
  1ef8abd

• Simple improvement to the alignment subworkflow.

  mkcmkc

  committed
  b2c2ad7

Commits on Feb 13, 2024

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

  mkcmkc

  committed
  f377861

• Updgrading from bwa mem to bwa mem2.

  mkcmkc

  committed
  0151004

• Fixing read group flag for bwa mem2.

  mkcmkc

  committed
  8456695

• Reassigning TODO.

  mkcmkc

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  c3f9050

• Emiting versions.

  mkcmkc

  committed
  fe49cf0

• Updating TODOs.

  mkcmkc

  committed
  1d13b56

• Fixing tags for new processes.

  mkcmkc

  committed
  8ce78ff

• Setting up targeted and wgts workflows for testing.

  Show description for ee059ad
  mkcmkc

  committed
  ee059ad

Commits on Feb 14, 2024

• Minor fixes and style improvements.

  mkcmkc

  committed
  e3f8d45

Commits on Feb 15, 2024

• Adding a TODO.

  mkcmkc

  committed
  58ed71c

Commits on Feb 18, 2024

• Add has_umis switch to markdups.

  mkcmkc

  committed
  de77de8

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

  mkcmkc

  committed
  01ad68d

• Change name of output bam from markdups.

  mkcmkc

  committed
  df6e65a

Commits on Feb 19, 2024

• Fix read group arg to bwa mem2.

  mkcmkc

  committed
  a4a95b1

• Add TODO.

  mkcmkc

  committed
  61aa1b1

• Fix markdups umi flags for TSO500 panel samples.

  mkcmkc

  committed
  a1dde8e

• Add TODO.

  mkcmkc

  committed
  8f06a9f

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

  mkcmkc

  committed
  a2330b2

• Running with umis for targeted and without for wgts.

  mkcmkc

  committed
  36c96fc

• Fix includes in targeted.nf.

  mkcmkc

  committed
  c8cec75

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

  mkcmkc

  committed
  b45b43a

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

  mkcmkc

  committed
  2479229

Commits on Feb 20, 2024

• Add TODO.

  mkcmkc

  committed
  00bf6ee

• Move new params into nextflow.config.

  mkcmkc

  committed
  3b83265

• Add label to markdups process.

  mkcmkc

  committed
  00cfe50

Commits on Feb 21, 2024

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

  mkcmkc

  committed
  ba241d1

• Use fastp by default.

  mkcmkc

  committed
  3c18154

• Remove bwa mem process.

  mkcmkc

  committed
  6b4f805

• Remove obsolete TODOs.

  mkcmkc

  committed
  c132e2b

• Pass ref genome version to markdups.

  mkcmkc

  committed
  ec992f1

• Add TODO.

  mkcmkc

  committed
  f7d3e5c

Commits on Feb 22, 2024

• Get versions from CLIs.

  mkcmkc

  committed
  a01df62

• Delete Dockerfiles and update containers to biocontainer equivalents.

  mkcmkc

  committed
  2c298c4

• Removing temp config.

  mkcmkc

  committed
  33244d9

• Fix process tags.

  mkcmkc

  committed
  8d82bac

• Reassign TODO.

  mkcmkc

  committed
  be271bb

• Add TODO.

  mkcmkc

  committed
  1364c8b

Commits on Feb 23, 2024

• Align read group construction with HMF pipeline5.

  mkcmkc

  committed
  e35e4f3

• Bump MarkDups to 1.1.1

  scwatts

  committed
  aa77b22

Commits on Feb 28, 2024

• Patch

  scwatts

  committed
  1301932

• Fix join for alignment BAM and corresponding BAIs

  scwatts

  committed
  0b27c4a

• Improve comments, syntax, etc

  scwatts

  committed
  0ca87ec

Commits on Feb 29, 2024

• Implement RNA alignment

  scwatts

  committed
  51e21b5

• Move, rename bwa-mem2 module

  scwatts

  committed
  3220f7b

• Fix bwa-mem2 process name

  scwatts

  committed
  b9e88fe

• Set STAR process label to 'process_high'

  scwatts

  committed
  781d883

• Fix incomplete container URL for SAMtools sort

  scwatts

  committed
  063aa3a

• Handle when read count less than max read split

  scwatts

  committed
  914edab

• Correctly format RG arg for STAR

  scwatts

  committed
  2d8c76c

• Fix bwa-mem2 bi-index variable name typo

  scwatts

  committed
  8749d45

• Adjust, fix bwa-mem2 index handling

  scwatts

  committed
  de1aad0

• Remove deprecated MarkDups -multi_bam argument

  scwatts

  committed
  7e0fb7f

• Fix AMBER subworkflow TN mode

  scwatts

  committed
  f47f33e

• Fix COBALT subworkflow TN mode

  scwatts

  committed
  08a58c8

• Adjust indentation

  scwatts

  committed
  c53ac44

• Fix SAGE calling subworkflow TN mode

  scwatts

  committed
  df1f5b7

• Improving handling of 'no merge' RNA BAM scenarios

  scwatts

  committed
  752f57a

• Set outputs for alignment workflows

  scwatts

  committed
  c648028

• Add missing channel docs

  scwatts

  committed
  db6bbf2

• Further work on RNA BAM handling

  scwatts

  committed
  c1f3142

• Use explicit returns in .branch ops

  scwatts

  committed
  bd45719

• Do not index RNA BAMs prior to merge

  scwatts

  committed
  8d06484

Commits on Mar 5, 2024

• Remove obsolete TODOs

  mkcmkc

  committed
  c7e87c2

Commits on Mar 7, 2024

• Fix Isofox singularity container URL

  scwatts

  committed
  1653daf

• Bump TSO500 data bundle version

  Show description for f618283
  scwatts

  committed
  f618283

• Remove -force_pathogenic_pass in PAVE somatic

  scwatts

  committed
  2bd379c

Commits on Mar 16, 2024

• Correct prepare reference panel data path lookup

  scwatts

  committed
  f76f79b

• Merge branch 'dev' into alignment-subworkflow

  scwatts

  committed
  07117c2

• Fix optional channel placeholders

  scwatts

  committed
  9b012d0

• Update modules.json

  scwatts

  committed
  b90c572

• Adjust indenting

  scwatts

  committed
  77b8bce

Commits on Mar 18, 2024

• Use standard container directive format for STAR

  scwatts

  committed
  bd6b304

• Add missing imports and subworkflow descriptions

  scwatts

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  c7f1774

Commits on Mar 19, 2024

• Use Bioconda/BioContainers for bwa-mem2 module

  scwatts

  committed
  177bf69

Commits on Mar 27, 2024

• Improve naming for bwa-mem2 output BAMs

  scwatts

  committed
  9d61690

Commits on Apr 15, 2024

• Use BAM index created during alignment

  scwatts

  committed
  066c8d2

Commits on Apr 22, 2024

• Improve BAM index selection

  scwatts

  committed
  0abc35f

• Include BAI in bwa-mem2/align stub

  scwatts

  committed
  eb95b4f

• Adjust input selection logic

  scwatts

  committed
  4039507

Commits on Apr 23, 2024

• Bump MarkDups to 1.1.5

  scwatts

  committed
  e8f6c99

• Remove Sambamba index module file

  scwatts

  committed
  ed8e1d1

• Add new meta.yaml

  scwatts

  committed
  e0da20a