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Updrate main with dev #27

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wants to merge 43 commits into from
Closed

Updrate main with dev #27

wants to merge 43 commits into from

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mberacochea
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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
  • 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>).
  • README.md is updated (including new tool citations and authors/contributors).

Ge94 and others added 30 commits September 2, 2024 15:44
@Ge94
Addition of long-reads pre-assembly qcs
2a6c062
@Ge94
Adapt params to short/long reads workflows
76e8d01
@Ge94
Debug missed parameters
bf547ff
@Ge94
Remove extra parameters from tests
7982339
@Ge94
Remove extra parameter from test
70bef02
@Ge94
Add ref genome folder to schema
120d5fe
@mberacochea
WIP - Restructure the pipeline to support Long Reads and Short Reads
2c2faa9
@mberacochea
Remove debug println statements
0ef2e63
@KateSakharova
add dbs links
48aa4ee
@Ge94
Add db generation instructions to README
ea24e1f
@KateSakharova
Merge pull request #18 from EBI-Metagenomics/fix-readme
4ca1e27 
add dbs links
@SandyRogers
Bugfix/assembler memory (#19)
d63ce26
@Ge94
LR-SR miassembler merge working
1fc455f
@Ge94
Resolved conflicts
d129cef
@Ge94
Updated conflict params and flags after merging
8fd885c
@Ge94
Fixed tests, refined variables, harmonised SR+LR
123ffbc
@Ge94
Updated reference_genome param
d95f0e5
@mberacochea
Remove puthi.conf file that was pushed by accident.
3cc1d79
@mberacochea
Merge pull request #17 from EBI-Metagenomics/feature/long_reads_suppo…
301aea1 
…rt_structure_refactor

Feature/long reads support structure refactor
@Ge94
Update raw_reads qc script with json parser
2379cb7
@Ge94
Comment and update --platform
d43a862
@Ge94
Minor refinements and documentation
c2a2bb6
@Ge94
Resolve conflicts
7b34057
@Ge94
Fixed tests and configs
aa18aa0
@mberacochea
Merge pull request #16 from EBI-Metagenomics/feature/long_read_qc
36f9c8e 
Addition of long-reads pre-assembly qcs
amended filter ratio threshold to 10%
9a3cf9f
@jmattock5
Update nextflow_schema.json
8aa06e7 
Changed ratio threshold default to 0.1 and amended description
@jmattock5
Merge pull request #22 from EBI-Metagenomics/filter_operator
686fe47 
Filter operator fix
@mberacochea
WIP - EBI FIRE S3 module for embargoed data
703c0c7
@mberacochea
Fire - private study - test case works on my laptop :)
2e51c92
@mberacochea
Add docs around private studies and one shallow test
f97e774
@mberacochea
Merge dev
38310c5
@mberacochea
Adjust the version on the wf metadata
dfaffba
@mberacochea
Massive commit, sorry about that.
eb26726 
nf-core linting + fixes all over the place to follow sensible nf-core linting rules
Updates multiqc and blastn
Enabled a nf-core linting github action
Tweaked the tests slightly (I think they are still failling .. testing and fixing ATM)
Upgraded to nf-schema 2.0.2 - also pinned this dependency
Remove check_max and moved to resources limits (require nextflow 24.0.0 as min - which I've set on the config)
Created some missing .diff for some modules
@mberacochea
Adjust code based on feedback
ebb5278
@mberacochea
Adjust code based on feedback
48cc7ee
@mberacochea
Add nf-core version to .nf-core.yml
a244fa0
@mberacochea
Bump version of nf-test for nf_tests github aciton
5592bc4
@mberacochea
Adjust test - megahit with empty contigs will succedd
e421639
@mberacochea
Merge pull request #23 from EBI-Metagenomics/feature/private-fire-sup…
5e53151 
…port

Feature/private fire support
@mberacochea
Merge branch 'dev' into feature/single-coverage-and-coverage-depth
f29e229
@mberacochea
Retrofit some fixes
5700593
@mberacochea
Merge pull request #28 from EBI-Metagenomics/feature/single-coverage-…
71685fd 
…and-coverage-depth

Feature/single coverage and coverage depth
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5 participants
@mberacochea @Ge94 @KateSakharova @SandyRogers @jmattock5