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Candidate for 0.4.0 #59

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merged 90 commits into from
Oct 6, 2024
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cefe885
Added orthofinder
GallVp Jun 17, 2024
be19f59
Added orthofinder_annotations param
GallVp Jun 18, 2024
10164c8
Fixed spellings
GallVp Jun 19, 2024
735a823
Updated modules and subworkflows
GallVp Jun 19, 2024
23e0b56
Fixed liftoff failure when lifting off from a single reference
GallVp Jun 19, 2024
ad20b4b
Added evaluation by BUSCO
GallVp Jun 19, 2024
39aeab5
Added pattern to busco_lineage_datasets
GallVp Jun 20, 2024
7049e0b
Fixed fasat/gff fead for busco
GallVp Jun 20, 2024
43db2ce
Included common tax ids for eggnog mapper
GallVp Jun 20, 2024
c3895cc
Added versions from GFF_STORE sub-workflows
GallVp Jun 20, 2024
9970b35
Implemented hierarchical naming scheme: geneI.tJ, geneI.tJ.exonK, gen…
GallVp Jun 20, 2024
df2183f
Updated contributors
GallVp Jun 20, 2024
cfa93b3
Now sorting list of bam and list of fastq before cat to avoid resume …
GallVp Jun 20, 2024
48e3e29
Renamed external_protein_fastas param to protein_evidence
GallVp Jun 20, 2024
0d14d97
Allowed BAM files for RNA evidence
GallVp Jun 21, 2024
f325bbd
Added GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES sub-workflow
GallVp Jun 24, 2024
2d7f9a5
Updated fastq_fastqc_umitools_fastp
GallVp Jun 24, 2024
343ed20
Changed orthofinder_annotations from FASTA/GFF to protein FASTA
GallVp Jun 25, 2024
70f34d0
Renamed braker_allow_isoforms param to allow_isoforms
GallVp Jun 25, 2024
587c169
Added param to turn on/off strict model purging by TSEBRA
GallVp Jun 25, 2024
183e5d0
Added top level subworkflow paths to module config blocks
GallVp Jun 26, 2024
088c3d6
Refactored GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST subworkflow
GallVp Jun 26, 2024
0ea16a6
Added param filter_liftoff_by_hints
GallVp Jun 26, 2024
6bb61d4
Updated flowchart
GallVp Jun 26, 2024
91b22f2
Updated flowchart
GallVp Jun 26, 2024
93ff754
Updated flowchart
GallVp Jun 26, 2024
6a02807
Now publishing more outputs
GallVp Jul 1, 2024
6d958bf
Added a script to automatically check module version updates
GallVp Jul 24, 2024
e07c595
Updated contributors
GallVp Jul 24, 2024
72a6423
Removed dependency on kherronism repo for BRAKER3 and REPEATMASKER
GallVp Jul 25, 2024
9cb7c62
Updated modules and sub workflows
GallVp Jul 26, 2024
bb6b1c6
Removed dependency on PlantandFoodResearch/nxf-modules
GallVp Jul 26, 2024
3ec77a3
Added missing nf-core moduels
GallVp Jul 26, 2024
4e3004f
Reduced BRAKER3 threads to 8
GallVp Aug 6, 2024
ac4c14f
Now the final annotations are stored in the annotations folder
GallVp Aug 6, 2024
c85852a
Updated test data paths
GallVp Aug 7, 2024
230448f
Added -gff flag to REPEATMASKER to save the gff file
GallVp Aug 7, 2024
b5c4229
Added a test profile based on public data
GallVp Aug 15, 2024
60aba33
Fixed CI
GallVp Aug 15, 2024
10fc01c
Renamed the pipeline
GallVp Aug 15, 2024
22304ec
Added disk clean-up before ci test
GallVp Aug 15, 2024
2dc213b
Simplified test file
GallVp Aug 16, 2024
3e1e801
Updated test params
GallVp Aug 19, 2024
89f53e8
Merge pull request #56 from PlantandFoodResearch/tests/public
GallVp Aug 19, 2024
cea7bae
Merge branch 'dev' into rename
GallVp Aug 19, 2024
402063d
More renaming
GallVp Aug 19, 2024
d8aa380
Merge pull request #57 from PlantandFoodResearch/rename
GallVp Aug 19, 2024
50ed8e8
initial template build from nf-core/tools, version 2.14.1
GallVp Aug 19, 2024
7c32d49
Added nf-core template
GallVp Aug 19, 2024
c122e62
Stub test is now passing again
GallVp Aug 19, 2024
51b7482
Fixed multiple linting issues
GallVp Aug 20, 2024
d1bc3ce
Updated README and flowchart
GallVp Aug 20, 2024
f94ff82
Updated tool list and contributors
GallVp Aug 23, 2024
2baea7f
Reduced image dpi to 300
GallVp Aug 23, 2024
e94e37c
Updated modules and subworkflows
GallVp Aug 23, 2024
a31ba79
Added info for outputs
GallVp Aug 23, 2024
806c7cf
Updated deps and parameters docs
GallVp Sep 10, 2024
99eb4ae
Updated output.md
GallVp Sep 10, 2024
8a64bee
Added outputs for RNAseq alignment
GallVp Sep 10, 2024
78a3553
Added outputs for Annotation with BRAKER
GallVp Sep 11, 2024
8509069
Updated outputs doc
GallVp Sep 12, 2024
024417d
Fixed linting
GallVp Sep 12, 2024
7c35254
Completed the output doc
GallVp Sep 12, 2024
274f697
Partially completed the usage doc
GallVp Sep 13, 2024
ab8fe9e
Added to usage doc
GallVp Sep 13, 2024
ca0d3bb
Completed docs and updated stub test
GallVp Sep 13, 2024
75c629c
Updated modules
GallVp Sep 13, 2024
3e00ad6
Updated modules
GallVp Sep 13, 2024
ffccf53
Fixed linting issues
GallVp Sep 13, 2024
19cdd3c
Added parameter add_attrs_to_proteins_fasta
GallVp Sep 20, 2024
5f16a82
Added nonmasked test case
GallVp Sep 23, 2024
75b66fd
Added a check for input assembly size
GallVp Sep 23, 2024
5d419b8
Now skipping file size check for stub run
GallVp Sep 25, 2024
2c79787
Updated flowchart
GallVp Sep 26, 2024
5bf2411
Updated flowchart
GallVp Sep 26, 2024
b750053
Updated modules
GallVp Sep 26, 2024
43776a3
Updated schema and params doc
GallVp Sep 26, 2024
c11b878
Updated PFR params
GallVp Sep 26, 2024
3eb9ace
Added benchmark column to the input sheet and used GFFCOMPARE to perf…
GallVp Sep 27, 2024
287916e
Updated input schema and stub test
GallVp Sep 27, 2024
745bae8
Updated pfr params
GallVp Sep 27, 2024
bd6bb64
Changed org caps
GallVp Sep 27, 2024
2768d40
Fixed linting
GallVp Sep 27, 2024
320b07a
Updated modules
GallVp Sep 27, 2024
b8b4d5a
Now REPEATMASKER GFF output is saved via CUSTOM_RMOUTTOGFF3
GallVp Sep 29, 2024
504b3a8
Added multiple tests to ci
GallVp Sep 29, 2024
c7ebfdc
Added SEQKIT_RMDUP to detect duplicate sequence and wrap the fasta to…
GallVp Sep 29, 2024
0c0269c
Added PFR instructions
GallVp Sep 29, 2024
6ec662c
Updated parameter section labels
GallVp Oct 4, 2024
0acb62b
Bumped version to 0.4.0
GallVp Oct 4, 2024
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Fixed liftoff failure when lifting off from a single reference
GallVp committed Jun 19, 2024
commit 23e0b56d3b2c1665e449239d38ceafbafee3be66
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Fixed`

1. Fixed BRAKER spellings [#36](https://github.com/PlantandFoodResearch/pangene/issues/36)
2. Fixed liftoff failure when lifting off from a single reference [#40](https://github.com/PlantandFoodResearch/pangene/issues/40)

### `Dependencies`

2 changes: 1 addition & 1 deletion conf/modules.config
Original file line number Diff line number Diff line change
@@ -263,7 +263,7 @@ process {
}

process {
withName: '.*:FASTA_GFFF_ORTHOFINDER:EXTRACT_PROTEINS' {
withName: '.*:FASTA_GFF_ORTHOFINDER:EXTRACT_PROTEINS' {
ext.args = '-y'
ext.prefix = { "${meta.id}.pep" }
}
7 changes: 6 additions & 1 deletion subworkflows/local/fasta_liftoff.nf
Original file line number Diff line number Diff line change
@@ -98,7 +98,12 @@ workflow FASTA_LIFTOFF {
[]
)

ch_merged_gff = MERGE_LIFTOFF_ANNOTATIONS.out.gff.mix(ch_merge_inputs.one)
ch_merged_gff = MERGE_LIFTOFF_ANNOTATIONS.out.gff
| mix(
ch_merge_inputs.one
| map { meta, gffs -> [ meta, gffs[0] ] }
// Unlist the upstream groupTuple
)
ch_versions = ch_versions.mix(MERGE_LIFTOFF_ANNOTATIONS.out.versions.first())

// COLLECTFILE: Transcript level kill list
File renamed without changes.