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Reffurbish mqc implementation #139

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Reffurbish mqc implementation #139

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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/viralgenie branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

Joon-Klaps and others added 23 commits June 12, 2024 09:53
@Joon-Klaps
temp efactor
c6f7599
@Joon-Klaps
Refactor multiqc_config.yml and mmseqs_annotate.nf files
37f1d2d
@Klaps-bot
[automated] Update CHANGELOG.md
0a78b89
@Joon-Klaps
Merge branch 'dev' into 113-include-coverage-plot-in-mqc
eb63052 
Signed-off-by: Joon Klaps <[email protected]>
@Joon-Klaps
Adding check if exists back
e7458bc
@Joon-Klaps
chore: Include bed file in BAM_STATS_METRICS workflow
dd12fb0
@Joon-Klaps
fix naming convention
48c200b
@Joon-Klaps
continuing on making the bed files
fbf4be7
@Joon-Klaps
chore: Refactor code to include gzipped bed files in read_file_to_dat…
5c37084 
…aframe function
@Joon-Klaps
WE DID IT! 🤌
1c6cda1
@Joon-Klaps
wir shaffen das 🙌 (almost)
12cd177
@Joon-Klaps
missing mqc file
303738b
@Joon-Klaps
Refactor column names and add new column in custom_multiqc_tables.py
0ab9e1a
@Joon-Klaps
adding the additional filtering step
386935b
@Joon-Klaps
remove typing of input variables
075b7c0
@Joon-Klaps
Merge branch 'dev' into 113-include-coverage-plot-in-mqc
42fb241 
Signed-off-by: Joon Klaps <[email protected]>
@Joon-Klaps
Merge branch 'dev' into 113-include-coverage-plot-in-mqc
3bd390d 
Signed-off-by: Joon Klaps <[email protected]>
@Joon-Klaps
update mqc & mqc logo
7edb54b
@Joon-Klaps
Merge branch '113-include-coverage-plot-in-mqc' of https://github.com…
15bfd2b 
…/Joon-Klaps/viralgenie into contig-read-distribution-mqc
@Klaps-bot
[automated] Update CHANGELOG.md
76169ba
@Joon-Klaps
linitngin nf-core
c799cb4
@Joon-Klaps
Merge branch 'reffurbish-mqc-implementation' of https://github.com/Jo…
0a71ad3 
…on-Klaps/viralgenie into reffurbish-mqc-implementation
@Joon-Klaps
continue customising summary of clusters
eccaa01
@Joon-Klaps
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collapse constrain & itvariant-calling for mapping results again.

Joon-Klaps and others added 30 commits October 18, 2024 14:40
@Joon-Klaps
Trying to cleanly extract mqc data
53391b0
@Joon-Klaps
extracing mqc with multiqc library
999b7f7
@Joon-Klaps
continuing the struggle
317a570
@Joon-Klaps
further refactoring
c7d6a50
@Joon-Klaps
constrains mapping mqc implementation
7054aff
@Joon-Klaps
Adding custom values to gen stats
506b334
@Joon-Klaps
Removing a couple to do statements
d3fedf6
@Joon-Klaps
custom cluster summary
84ca446
@Joon-Klaps
Continue our custom results
5b11b9e
@Joon-Klaps
Remove unused metadata and summary files
24d2ae8
@Joon-Klaps
fixing run
a220eb7
@Joon-Klaps
nextflow language server debug
725a8be
@Joon-Klaps
typo
b4a6efa
@Joon-Klaps
sample filtering still not working
0882fa2
@Joon-Klaps
Filtering succesfull
f517766
@Joon-Klaps
reformatting workflow logic
a4dec32
@Joon-Klaps
Merge branch 'dev' into reffurbish-mqc-implementation
40f50d8 
Signed-off-by: Joon Klaps <[email protected]>
@Joon-Klaps
Fixing issues from language server
e0ccf5c
@Joon-Klaps
typo untarS
c56dccd
@Joon-Klaps
refactoring bin to more modular
2373473
@Joon-Klaps
debugging filter mqc table
6632187
@Joon-Klaps
MODULAR
69f7c03
@Joon-Klaps
removing unnecessary functions
c114915
@Joon-Klaps
Lots & lots of python refactoring
08c5fd8
@Joon-Klaps
removing redundant files
fe33b5c
@Joon-Klaps
adding empty declaration ch_clusters_tsv
cd01013
@Joon-Klaps
we have versions
59facde
@Joon-Klaps
mash gets reincluded
6c6edb9
@Joon-Klaps
remove uncessary line
08e5023
@Joon-Klaps
Fixing some more issues
33f817f
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@Joon-Klaps @Klaps-bot