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Add kraken2 phylogenetic assignment subworkflow #47

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@ctuni ctuni commented Oct 28, 2024 •
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Added a subworkflow for a "phylogenetic QC" that does kraken2 assignment for each sample and then plots them on an interactive krona plot. I have not added the kraken2 reports to multiqc, this should be the next step.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/seqinspector branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

mahesh-panchal and others added 30 commits March 19, 2024 10:09
@mahesh-panchal
Update assets/schema_input.json
56e01a0
@alneberg @Aratz
grop instead of project in a single place
6c94332 
Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
@alneberg @mahesh-panchal
Updated test profile input
4779844
@alneberg @KarNair
Update assets/schema_input.json
28e0137 
Co-authored-by: Karthik Nair <35717861+KarNair@users.noreply.github.com>
@alneberg
Merge pull request nf-core#2 from mahesh-panchal/input_workflow
d169eef 
Input workflow
@Aratz
Generate reports per lane, group and rundir
a31040e
@Aratz
Improve formatting
0da5870
@Aratz
Improve output sorting
d233d8f
@Aratz
Use group instead of project
307e43c
@Aratz
Fix output channel
627cf94
@Aratz
Fix linting
c9ba028
@Aratz
Give credits back to NGI
2cfc91d
@Aratz
Fix file names
fbfb02d
@Aratz
Set up tests
8a19929
@kedhammar
point test conf upstream
eba628e
@kedhammar
project -> group
23f69d1
@kedhammar
project -> group
1ebf3f1
@kedhammar
make lane non-compulsory
b0bf471
@kedhammar
remove unused file
9e0eca3
@kedhammar
revamp nf-test, run once for each sequencing platform
98e60bf
@Aratz
Update modules and subworkflows
d95c660
@Aratz
Fix multiqc extra files
e0527cc 
Issue with the previous implementation was that sometimes
MULTIQC_PER_LANE would execute before the extra files were collected
into `ch_multiqc_extra_files`, causing `null` to be added to the list of
files passed to multiqc.
@MatthiasZepper
Merge branch 'dev' into nf-core-template-merge-2.14.1
ba72067
@Aratz
Add test snapshots
42159a1
@Aratz
Remove unused module configuration
ef61f9f
@Aratz
Update usage docs and restore example samplesheet
51b01e9
@Aratz
Update output docs
7c7f31f
@Aratz
Update changelog
1c4f6e0
@Aratz
Update samplesheet in readme file
211bfaf
@Aratz
Merge pull request nf-core#15 from nf-core/nf-core-template-merge-2.14.1
e93baf9 
Important! Template update for nf-core/tools v2.14.1
adamrtalbot and others added 28 commits December 19, 2024 11:20
@adamrtalbot
Merge pull request nf-core#71 from adamrtalbot/fastqscreen_handles_mo…
1f7dc68 
…re_than_1_fastq_file

Patch fastqscreen to handle multiple input FASTQ files
@Aratz
Add skip tools parameter
4e30ba8
@Aratz
Add tests for skip_tools
5037949
@Aratz
Update docs
e48d5b7
@Aratz
Update CHANGELOG
e75d684
@Aratz
Fixed linting
af55550
@Aratz
Improve skip_tools regex pattern
868f8c2
@Aratz
Add option to skip fastqscreen and subsampling
439d747
@Aratz
Fix link to nf-core docs
ad6a2c4
@Aratz
Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…
4beba7a 
…-3.1.2.dev0
@Aratz
Set nf_core version to 3.1.1
e3c10e3
@Aratz
Remove double include of modules.config
2ab4fa0
@Aratz @mirpedrol
Update CITATIONS.md
78edd60 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
@Aratz @mirpedrol
Update README.md
5949098 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
@Aratz @mirpedrol
Update README.md
0a99588 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
@Aratz @mirpedrol
Update docs/output.md
84e15b0 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
@Aratz
Merge pull request nf-core#72 from nf-core/nf-core-template-merge-3.1…
4ed43fb 
….2.dev0

Important! Template update for nf-core/tools v3.1.2.dev0
@Aratz
Merge pull request nf-core#68 from Aratz/tool_selector
ec9570d 
Add skip tools parameter for tool selection
@Aratz
Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…
5d4686e 
…-3.1.2
@Aratz
Merge branch 'nf-core-template-merge-3.1.2' into nf-core-template-mer…
b259a87 
…ge-3.2.0
@Aratz
Merge pull request nf-core#74 from nf-core/nf-core-template-merge-3.2.0
826a811 
Important! Template update for nf-core/tools v3.2.0
@Aratz
Set up nft-utils in tests
734a412
@Aratz
Exclude fastqc/*_fastqc.html files
5053098
@Aratz
Update changelog
0372247
@Aratz
Merge pull request nf-core#75 from Aratz/nft-utils
80f0095 
Set up nft-utils in tests
@ctuni
Merge branch 'dev' into feature/kraken2
d251034
@ctuni
fixin jsons
06adb1e
@ctuni
fixed docs/output
2747578
@FranBonath FranBonath added this to the 1.1.0 milestone Nov 6, 2025
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@Aratz Aratz Awaiting requested review from Aratz

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add kraken2 to seqinspector