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Update of ExOrthist to DSL2 version and more #40

Merged
merged 89 commits into from
Dec 5, 2024
Merged

Update of ExOrthist to DSL2 version and more #40

merged 89 commits into from
Dec 5, 2024

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toniher
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@toniher toniher commented Dec 5, 2024

  • Upgrade to DSL2 version
  • Creation of different local modules for each process
  • Place the two pipelines as two workflows
  • Split main workflow into different subworkflows
  • Addition of schema validation
  • Easier to run process
  • General execution test for the main pipeline with nf-test
  • Inclusion of nf-core profiles for different institutions into the configuration

toniher and others added 30 commits October 10, 2024 10:39
@toniher
starting playing
5ecca74
@toniher
Adding nextflow_schema.json and carrying on
be9114a
@toniher
handle first module
665a800
@toniher
next file step
584a30f
@toniher
Cleaning a bit
fbe8817
@toniher
migration up to starting alignment
e61712b
@toniher
up to realign, need Python
80def29
@toniher
adding a pandas container
45fa2e9
@toniher
More modules added to align
cafc67b
@toniher
getting score matches
aef2307
@toniher
more modules migrated
3c12617
@toniher
moving more modules and new dockerfile
dcc302d
@toniher
upgrade modules and moving to different containers
816d181
@toniher
carry on R
26b5c83
@toniher
updated Dockerfile for R
c9007ae
@toniher
Moved everything to DSL2
6282203
@toniher
changed gitignore
a1bcd4e
@toniher
upgrade test github
49c6220
@toniher
start working on exint_plotter>
db81838
@toniher
fixes issues, now output is the same as in former version
8066ae8
@toniher
exint_nf almost migrated
8e7fded
@toniher
finished exint
c081079
@toniher
moved to subworkflow first part
437ec73
@toniher
moved another subworkflow
e5352e3
@toniher
moved all main to subworkflows
c8bdc4d
@toniher
moving plot as workflow
37e19d8
@toniher
some fixes to README
17b8230
@toniher
Update README.md
9427c9e
@toniher
more documenting
2612603
@toniher
help moved
a9fa4fd
toniher and others added 29 commits October 25, 2024 19:53
@toniher
adding tests
c09ec88
@toniher
minor stuff
179c956
@toniher
simplify
2626fe9
@toniher
upgrade
0f76808
@toniher
versions
967019c
@toniher
update README
bdf20d5
@toniher
move out and carry on
12e3750
@toniher
remove params.output
92093a5
@toniher
remove params.output
f531020
@toniher
fix missing param
a7a75a6
@toniher
more icons and moved to projectDir
3a991bf
@toniher
Handling extraexons
3dcc801
@toniher
Commented channel
eb1ced1
@toniher
minimal config changes
61780a5
@toniher
fixing outdir
3b75ed9
@toniher
rming unneeded params
df7e1d3
@toniher
adding actual dummy nofile for avoiding errors in some setups
6e79dbb
@toniher
changing output dir to former system, making everything publish
1b8b099
@toniher
Update README.md
a8f083c
@toniher
not publishing all files
244967d
@toniher
Update TODO.md
9832521
@toniher
Update README.md
992d66c
@toniher
Update CITATIONS.md
fdf46ae
@toniher
Update README.md
8a939b7 
minor typos
@fedemantica
Fix computation of seq sim in subroutine score_introns in B1
57c381a
@fedemantica
Create tmp folder in merge_aligns.nf if needed
5974a7c
@toniher
converting string to path for main output used in plot
5fa9398
@toniher
handling isoform_interesting_exs channel
478ca53
@fedemantica
Include derive_species.nf in plot.nf workflow
09c26df
@toniher toniher merged commit 83185dc into master Dec 5, 2024
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2 participants
@toniher @fedemantica