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Release candidate for 0.6.0 #129

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merged 42 commits into from
Dec 20, 2024
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c8667c9
Add EXTRACT_CDS feature to GFF_STORE workflow
liamlelievre Dec 4, 2024
dbebd7a
Update gff_store.nf
liamlelievre Dec 4, 2024
203af9b
Update gff_store.nf
liamlelievre Dec 4, 2024
13fe4e9
add EXTRACT_CDNA to gff_store.nf
liamlelievre Dec 4, 2024
c7bf40b
add GFF_STORE:EXTRACT_CDNA to modules.config
liamlelievre Dec 4, 2024
f0699a6
Update gff_store.nf
liamlelievre Dec 4, 2024
563bd13
Add cdna and cds outputs to output.md
liamlelievre Dec 4, 2024
79befa5
Add notes about cdna and cds update to CHANGELOG.md
liamlelievre Dec 4, 2024
47e2cf3
Added liamlelievre to contributors - README.md
liamlelievre Dec 4, 2024
2a118be
Update output.md
liamlelievre Dec 4, 2024
216225c
Added v0.6.0 notes to CHANGELOG.md
liamlelievre Dec 4, 2024
74cd2b2
removed trailing whitespace gff_store.nf
liamlelievre Dec 4, 2024
81871ff
Removed trailing whitespace - modules.config
liamlelievre Dec 4, 2024
3f898b0
rename params - modules.config
liamlelievre Dec 4, 2024
5af18c8
Rename params - nextflow.config
liamlelievre Dec 4, 2024
841ea02
Added code contributors
GallVp Dec 4, 2024
e05a469
Run nf-test successfully in minimal and stub
Dec 5, 2024
d2ff47e
Run nf-test successfully in minimal and stub, renamed attr, updated docs
Dec 5, 2024
2bcab04
Merge branch 'main' into add-gffread-feature
Dec 5, 2024
d21d70e
Add attributes option for -F -D to cds and cdna
Dec 5, 2024
9be84b2
Fixed linting issues
GallVp Dec 5, 2024
767239a
Updated snapshot
GallVp Dec 5, 2024
e042615
Fixed nextflow-setup version
GallVp Dec 5, 2024
43742fb
Fixed indent
GallVp Dec 5, 2024
17673f7
Merge pull request #119 from liamlelievre/add-gffread-feature
GallVp Dec 5, 2024
fb9a0f4
Fixed an issue where TSEBRA failed because LIFTOFF lifted non-protein…
GallVp Dec 4, 2024
87cf1dd
Updated snapshots
GallVp Dec 5, 2024
7d1f318
Updated changelog
GallVp Dec 5, 2024
e1cceba
Merge pull request #122 from Plant-Food-Research-Open/patch/121
GallVp Dec 5, 2024
b9b7d37
Fixed issues in genepal-report
GallVp Dec 10, 2024
496ff62
Merge pull request #126 from Plant-Food-Research-Open/patch/124
GallVp Dec 10, 2024
3114adb
Added parameter filter_genes_by_aa_length
GallVp Dec 10, 2024
d694431
Updated snapshots
GallVp Dec 10, 2024
0f7784c
Added test to verify that GFFREAD can filter mRNA by CDS length
GallVp Dec 11, 2024
f980772
Updated snapshots
GallVp Dec 11, 2024
ab3ae37
Updated README and snapshot
GallVp Dec 11, 2024
c65ebaa
Added 1 to filter_genes_by_aa_length to exclude stop codon from filte…
GallVp Dec 15, 2024
9759882
Merge pull request #127 from Plant-Food-Research-Open/feat/filter_gen…
GallVp Dec 15, 2024
fa28176
Fixed post-liftoff merge
GallVp Dec 16, 2024
2a0c7a2
Merge pull request #130 from Plant-Food-Research-Open/fix/mergefail
GallVp Dec 16, 2024
3459b40
Fixed short intron crash
GallVp Dec 19, 2024
d069633
Merge pull request #131 from Plant-Food-Research-Open/fix/short_intron
GallVp Dec 20, 2024
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Added code contributors
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GallVp authored Dec 4, 2024
commit 841ea020b7bcf632f6ce5a5ff1e30c8438c9ae89
6 changes: 5 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -97,7 +97,7 @@ sbatch ./pfr_genepal

plant-food-research-open/genepal workflows were originally scripted by Jason Shiller ([@jasonshiller](https://github.com/jasonshiller)). Usman Rashid ([@gallvp](https://github.com/gallvp)) wrote the Nextflow pipeline.

We thank the following people for their extensive assistance in the development of this pipeline:
We thank the following people for extensive assistance in the development of the pipeline,

- Cecilia Deng [@CeciliaDeng](https://github.com/CeciliaDeng)
- Charles David [@charlesdavid](https://github.com/charlesdavid)
@@ -107,6 +107,10 @@ We thank the following people for their extensive assistance in the development
- Susan Thomson [@cflsjt](https://github.com/cflsjt)
- Ting-Hsuan Chen [@ting-hsuan-chen](https://github.com/ting-hsuan-chen)

and for contributions to the codebase,

- Liam Le Lievre [@liamlelievre](https://github.com/liamlelievre)

The pipeline uses nf-core modules contributed by following authors:

<a href="https://github.com/gallvp"><img src="https://github.com/gallvp.png" width="50" height="50"></a>
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