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POC using module classes #1

Closed
wants to merge 26 commits into from
Closed

POC using module classes #1

wants to merge 26 commits into from

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mirpedrol
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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/multiplesequencealign 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).

mirpedrol added 26 commits August 28, 2024 15:05
@mirpedrol
install class expanded subworkflows
a409347
@mirpedrol
use class subworkflows
8b6c879
@mirpedrol
remove old - not needed - modules and subworkflows
a357e15
@mirpedrol
update all subworkflows
4f6cbbc
@mirpedrol
Merge pull request #2 from mirpedrol/update-class-subworkflows
0b6bdab 
Update all subworkflows
@mirpedrol
move evaluation subworkflow to an independent workflow
57c4e82
@mirpedrol
nextflow language server fixes and channel combination fixes
e2b92c1
@mirpedrol
remove toolsheet
3476d1f
@mirpedrol
add parameters to provide tool arguments and save results per tool+ar…
e4dd23f 
…gs folder with the file name being the sample
@mirpedrol
update methodsDescriptionText() according to the v3 template
8969f58
@mirpedrol
fix Nf language server errors and make evaluation workflow work
e6534cc
@mirpedrol
read previous downstream samplesheets and start updating schemas
056d141
@mirpedrol
update to nf-schema and read existing samplesheet to generate downstr…
be314b4 
…eam samplesheet
@mirpedrol
more fixes to make downstream samplesheet work + start adding params …
79a714f 
…to meta map
@mirpedrol
either alignment or guidetree + treealign
0ce16ed
@mirpedrol
not compress files + fixes to make the evaluation workflow work
d5810a8
@mirpedrol
add EXTRACT_STRUCTURES swf and fix downstream samplesheet
f0e8e0a
@mirpedrol
remove reference_genome_options from schema
529d22b
@mirpedrol
Merge pull request #3 from mirpedrol/evaluation-to-workflow
88e1a9c 
Move evaluation subworkflow to an independent workflow
@mirpedrol
update tcoffee/alncompare
7677fe2
@mirpedrol
update kalign/align
4371fb7
@mirpedrol
update mafft
55e7b75
@mirpedrol
update modules
9bae6c1
@mirpedrol
update all modules
8acb2c9
@mirpedrol
allow compressed msa for evaluation
86ad6e7
@mirpedrol
Merge pull request #4 from mirpedrol/update-modules
4300779 
Update modules
@mirpedrol
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Closing as outdated and includes unecessary work. The new POC PR is #6

@mirpedrol mirpedrol closed this Jan 29, 2025
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@mirpedrol