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initial pipeline pseudo PR #17

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initial pipeline pseudo PR #17

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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/proteinfamilies branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

vagkaratzas and others added 30 commits November 5, 2024 11:47
@vagkaratzas
modules installed
7a768c5
@vagkaratzas
input samplesheet update to fasta
821f73e
@vagkaratzas
clustering modules chained
84f8965
@vagkaratzas
nf-core createtsv test init
e5bc24f
@vagkaratzas
debugged targetdb copy by staging
1802206
@vagkaratzas
syncing samples by meta, module diffs
40e02f2
@vagkaratzas
EXECUTE_CLUSTERING subworkflow done
d362d9e
@vagkaratzas
Merge pull request #1 from vagkaratzas/createtsv-tests
af91b89 
Createtsv tests
@vagkaratzas
chunk_clusters nf and py init
0c56473
@vagkaratzas
cluster chunkcs complete
ace2dbd
@vagkaratzas
Merge pull request #2 from vagkaratzas/chunking_clusters
65381a7 
Chunking clusters
@vagkaratzas
seqera container for local python module
b1309f5
@vagkaratzas
clustering parameters added, chunking fasta instead of tsv to then fe…
a84dbe6 
…ed MSA tools
@vagkaratzas
removed pandas from chunking script, optimised for memory
2e46012
@vagkaratzas
msa input formatted, famsa run properly
f2983bc
@vagkaratzas
meta updated to chunks level, hmmbuild chained to workflow
6f52683
@vagkaratzas
HMMER_HMMSEARCH chained, inputs combined successfully on meta id, met…
2d48faf 
…a tags updated to chunk level
@vagkaratzas
minor publish path change
54f7a05
@vagkaratzas
hmmsearch evalue cutoff and output full MSA by default
5d9e7e9
@vagkaratzas
generate_families converted into subworkflow
a39d649
@vagkaratzas
mafft alternative alignment tool
e203af3
@vagkaratzas
hmmbuild updated
e24a63b
@vagkaratzas
added support for .gz input fasta
4c639f0
@vagkaratzas
Preparing input channel to extract family representative sequences fo…
b4a054f 
…r post-processing
@vagkaratzas
added clipkit module, fixing some linting warnings, updated subworkflows
2b6b4a8
@vagkaratzas
extract family reps script
c136435
@vagkaratzas
removed prokka module
5e068d1
@vagkaratzas
export fam to rep mapping
b0ee92d
@vagkaratzas
EXTRACT_FAMILY_REPS publishDir
82742e7
@vagkaratzas
Merge pull request #4 from vagkaratzas/prokka
8b444df 
exporting reps to fams mapping and fasta
vagkaratzas and others added 17 commits January 31, 2025 12:46
@vagkaratzas @jfy133
Update subworkflows/local/utils_nfcore_proteinfamilies_pipeline/main.nf
dd2cc97 
Co-authored-by: James A. Fellows Yates <[email protected]>
@vagkaratzas
checkIfExists: true added to file()
07d52a3
@vagkaratzas @jfy133
Update nextflow_schema.json
f6cb471 
Co-authored-by: James A. Fellows Yates <[email protected]>
@vagkaratzas @jfy133
Update nextflow.config
0ce6ee0 
Co-authored-by: James A. Fellows Yates <[email protected]>
@vagkaratzas @jfy133
Update docs/output.md
f050d84 
Co-authored-by: James A. Fellows Yates <[email protected]>
@vagkaratzas @jfy133
Update docs/usage.md
1b2d81b 
Co-authored-by: James A. Fellows Yates <[email protected]>
@vagkaratzas @jfy133
Update docs/output.md
921cf06 
Co-authored-by: James A. Fellows Yates <[email protected]>
@vagkaratzas
batch commit suggestions from james
bdc8627
@vagkaratzas
ch_ notation instead of set {}, .map changed to multiline everywhere,…
0ab063f 
… optional directory parameters added to output.md
@vagkaratzas
assets/samplesheet.csv added back
9be00f7
@vagkaratzas
modules and subworkflows moved to respective folders + env
e39a349
@vagkaratzas
prefix instead of meta.id for output naming in two of the local modules
f64c769
@vagkaratzas
only main author mail kept
d6e2e3e
@vagkaratzas
removed duplicate includeConfig 'conf/modules.config'
86cdb61
@vagkaratzas
interpretation of folder outputs in output.md, strict clustering thre…
99de435 
…sholds changed to 0.97
@vagkaratzas
help_text in most schema params
ada9368
@vagkaratzas
Merge pull request #23 from vagkaratzas/dev
acb9465 
Review points from James
@vagkaratzas vagkaratzas requested a review from jfy133 January 31, 2025 15:48
@vagkaratzas vagkaratzas marked this pull request as draft February 3, 2025 10:05
jfy133
jfy133 reviewed Feb 5, 2025
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Last couple of minor comments/edits, but I will approve this and the other PR

CHANGELOG.md Outdated
@@ -3,14 +3,16 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.0.0dev - [date]
## v1.0.0 - [2025/02/03]
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Suggested change
## v1.0.0 - [2025/02/03]
## v1.0.0 - [2025/02/05]

docs/output.md Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
subworkflows/local/utils_nfcore_proteinfamilies_pipeline/main.nf Outdated Show resolved Hide resolved
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@jfy133 jfy133 jfy133 left review comments

@edmundmiller edmundmiller edmundmiller approved these changes

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@vagkaratzas @jfy133 @edmundmiller @mberacochea @nf-core-bot