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Implement alignment subworkflow #6

Merged
merged 87 commits into from
Apr 24, 2024
Merged

Implement alignment subworkflow #6

merged 87 commits into from
Apr 24, 2024

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scwatts
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@scwatts scwatts commented Mar 12, 2024

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scwatts and others added 30 commits December 1, 2023 18:33
@scwatts
Basic isolated alignment subworkflow outline
86220ec
@mkcmkc
Initial implementation of alignment workflow.
4e92135
@mkcmkc
Simplified condition on whether fastp is run in alignment subworkflow.
f69caf9
@mkcmkc
Get rid of blocking when merging individual sample records back into …
1ef8abd 
…a single group record.
@mkcmkc
Simple improvement to the alignment subworkflow.
b2c2ad7
@mkcmkc
Merge alignment and markdups logic into Stephen's stubs.
f377861
@mkcmkc
Updgrading from bwa mem to bwa mem2.
0151004
@mkcmkc
Fixing read group flag for bwa mem2.
8456695
@mkcmkc
Reassigning TODO.
c3f9050
@mkcmkc
Emiting versions.
fe49cf0
@mkcmkc
Updating TODOs.
1d13b56
@mkcmkc
Fixing tags for new processes.
8ce78ff
@mkcmkc
Setting up targeted and wgts workflows for testing.
ee059ad 
+ Put read_alignment and read_processing subworkflows into targeted workflow.
+ Uncomment the whole wgts worflow and integrate this with the read_alignment and read_processing subworkflows.
@mkcmkc
Minor fixes and style improvements.
e3f8d45
@mkcmkc
Adding a TODO.
58ed71c
@mkcmkc
Add has_umis switch to markdups.
de77de8
@mkcmkc
Force symlink overwrite so process does not fail on resume.
01ad68d
@mkcmkc
Change name of output bam from markdups.
df6e65a
@mkcmkc
Fix read group arg to bwa mem2.
a4a95b1
@mkcmkc
Add TODO.
61aa1b1
@mkcmkc
Fix markdups umi flags for TSO500 panel samples.
a1dde8e
@mkcmkc
Add TODO.
8f06a9f
@mkcmkc
Fix read group extraction from fastq filenames and a bug in the markd…
a2330b2 
…ups stub.
@mkcmkc
Running with umis for targeted and without for wgts.
36c96fc
@mkcmkc
Fix includes in targeted.nf.
c8cec75
@mkcmkc
Only run markdups with UMIs when tso500 panel is selected.
b45b43a
@mkcmkc
Create switch between bwa mem and bwa mem2 for debugging purposes.
2479229
@mkcmkc
Add TODO.
00bf6ee
@mkcmkc
Move new params into nextflow.config.
3b83265
@mkcmkc
Add label to markdups process.
00cfe50
@scwatts scwatts added this to the Release 1.0.0 milestone Mar 12, 2024
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github-actions bot commented Mar 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0da20a

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  45 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 0.3.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in main.nf: System.exit(1) [line 44]
  • system_exit - System.exit in main.nf: System.exit(1) [line 46]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 33]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 49]
  • system_exit - System.exit in WorkflowOncoanalyser.groovy: System.exit(1) [line 62]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 29]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 39]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 47]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 55]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 63]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 68]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 84]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 89]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 108]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 113]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 121]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 182]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 263]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 275]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 283]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 290]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 298]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 313]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 344]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 116]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 123]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 130]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 144]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 154]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 159]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 172]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 188]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 197]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-23 05:48:52

@scwatts
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scwatts commented Apr 23, 2024

I've completed testing on the alignment subworkflow using simulated DNA/RNA reads representing four patients across WGTS data and targeted data:

  • subject_a (WGTS): tumor/normal DNA, tumor RNA
  • subject_b (WGTS): tumor/normal DNA, tumor RNA
  • subject_c (targeted, TSO500): tumor DNA, tumor RNA
  • subject_d (targeted, TSO500): tumor DNA, tumor RNA

Each subject where applicable contained:

  • somatic SV resulting in a reportable gene fusion
  • viral integration
  • one driver somatic small variant
  • one predisposing germline small variant
  • random somatic small variants
  • population heterozygous small variants (present in both tumor and normal)

NB: RNA data supported only the fusion event

Using this simulated data, I performed a total of 132 oncoanalyser runs that covered common input combinations drawing from the following options for each sample:

  • BAM, MarkDups duplicate marking
  • BAM, GATK4 duplicate marking
  • FASTQ, single lane + single library
  • FASTQ, single lane + multiple library
  • FASTQ, multiple lane + single library
  • FASTQ, multiple lane + multiple library

Combinations were additionally selected to cover all relevant analysis types. Each input combination was also tested against the following:

  • Sample number (single/multiple)
  • FASTQ splitting (default/disabled)
  • Mode (WGTS/targeted)

The outputs of each oncoanalyser run was compared to ensure expected features were present with identical metrics e.g. depth, location, fusion partners, etc (population hets were excluded from comparison). No differences in these comparisons were observed.

/cc @charlesshale @mkcmkc

@scwatts scwatts marked this pull request as ready for review April 23, 2024 22:49
@scwatts scwatts requested a review from charlesshale April 23, 2024 22:49
charlesshale
charlesshale approved these changes Apr 24, 2024
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Approved

@scwatts scwatts merged commit 101e987 into dev Apr 24, 2024
4 checks passed
@scwatts scwatts deleted the alignment-subworkflow branch April 24, 2024 01:28
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale @bounlu @mkcmkc