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from megafusion to vcf_collect #414

Merged
merged 55 commits into from
Nov 20, 2023
Merged

from megafusion to vcf_collect #414

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1ea68bc
from megafusion to vcf_collect
rannick Sep 29, 2023
da68e1d
start collecting more information with vcf_collect
rannick Oct 2, 2023
42679f7
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Oct 2, 2023
385b05a
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Oct 23, 2023
41bd823
add hgnc id and extra info for vcf file
rannick Oct 30, 2023
4ba9728
add hgnc id and extra info for vcf file
rannick Oct 30, 2023
cd2b4ee
fix merging conflicts
rannick Oct 30, 2023
b0c0f18
fix channel i/o
rannick Oct 30, 2023
605280b
black
rannick Oct 30, 2023
36519af
fix bug in channel i/o
rannick Oct 30, 2023
fd80774
fix bug in channel i/o
rannick Oct 30, 2023
3db4665
add hgnc download to build_references workflow
rannick Oct 30, 2023
71b15d5
add hgnc download to build_references workflow
rannick Oct 30, 2023
52bf004
add meta info for hgnc
rannick Oct 30, 2023
b07cee3
update gtfparse containers
rannick Oct 31, 2023
bdb1a6e
fix bug with param genome.s
rannick Oct 31, 2023
aa74611
add AGAT/CONVERTSPGFF2TSV to convert gtf to tsv
rannick Nov 1, 2023
7a516b9
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Nov 6, 2023
cc4ec30
install agat/convertspgff2tsv from nf-core
rannick Nov 6, 2023
0c3ffae
correct typo
rannick Nov 6, 2023
ba55fa3
vcf_collect takes tsv_coding_effect channel instead of tsv
rannick Nov 6, 2023
1b9c181
remove empty entry
rannick Nov 6, 2023
775444e
make optional gtf and coding effectsg
rannick Nov 6, 2023
4a38147
remove HGNC: from HGNC id column
rannick Nov 6, 2023
6f2a4ea
fix hgnc date timestamping
rannick Nov 6, 2023
f4c0912
black
rannick Nov 6, 2023
4337f4a
add support for case fusioninspector filters out a fusion from fusion…
rannick Nov 7, 2023
3736e69
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Nov 7, 2023
be99aef
update changelog
rannick Nov 8, 2023
3c1a8d5
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Nov 8, 2023
1c109ff
Update bin/vcf_collect.py
rannick Nov 10, 2023
ff51b1c
Apply suggestions from code review
rannick Nov 10, 2023
92a3dad
use fstrings
rannick Nov 13, 2023
7a700f0
add info on GTF output file from fusioninspector
rannick Nov 13, 2023
00d12a2
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Nov 13, 2023
22e4502
black
rannick Nov 13, 2023
a2b485f
Merge branch 'megafusion_to_vcf_collect' of https://github.com/nf-cor…
rannick Nov 13, 2023
e59823c
fix header typer
rannick Nov 13, 2023
afda8fd
mend
rannick Nov 13, 2023
f14bd90
Revert "mend"
rannick Nov 13, 2023
55d95d1
revert to plain pandas container
rannick Nov 13, 2023
6bc7351
sample should just be meta.id, add fusion_data in module for output name
rannick Nov 13, 2023
d559232
remove quotes and flatten the pseudo list in annots
rannick Nov 13, 2023
d0a4bf2
back to original container
rannick Nov 13, 2023
b468942
revert to pandas
rannick Nov 13, 2023
960db4c
apply fixes
rannick Nov 14, 2023
3084301
Merge branch 'dev' into megafusion_to_vcf_collect
rannick Nov 15, 2023
852c6ac
compress vcf output
rannick Nov 15, 2023
7801cab
Merge branch 'megafusion_to_vcf_collect' of https://github.com/nf-cor…
rannick Nov 15, 2023
9643ed8
black
rannick Nov 15, 2023
bb703dd
modules updatge
rannick Nov 15, 2023
ef9f57a
move compression out of vcf_collect
rannick Nov 15, 2023
f33a5e9
fix ,/;
rannick Nov 15, 2023
a8b0743
fix values display vcf
rannick Nov 16, 2023
acf64a1
add hgnc id for fusionreport-only entries in vcf and add bug fix
rannick Nov 17, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424)
- `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426)
- `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429)
- Change megafusion into vcf_collect, taking into account e.g. the annotation and coding effects outputs from fusioninspector, HGNC ids, frame status... [#414](https://github.com/nf-core/rnafusion/pull/414)
- CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430)
- Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432)
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202 changes: 0 additions & 202 deletions bin/megafusion.py
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