merge the lncpipe:dev to original LncPipe:dev #36 - #37

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likelet wants to merge 126 commits into

likelet:devfrom

Commits on Mar 20, 2025

test commit
ctuni
committed
a85ac93

Commits on Mar 24, 2025

the pipeline now reads a samplesheet!
ctuni
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4b70ac5
adding the github related files
ctuni
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797d272
finish
ctuni
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432a41f
forgot a file
ctuni
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fd7385b
trying to pass tests
ctuni
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33d4f7e
regenerated logo
ctuni
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7c44772
resetting logo
ctuni
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f250cdb
testing
ctuni
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acf741b
testing
ctuni
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e9c8792
test
ctuni
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d26430e
test
ctuni
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087841a
?
ctuni
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7b2b787
regenerate logo
mirpedrol
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c6f4a4d
Merge pull request #73 from ctuni/feature/github_actions
ctuni
authored
6496ed4
Merge branch 'dev' into feature/input_samplesheet
ctuni
authored
34e6ba0
fixing mistake
ctuni
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bfc629c
added structure based on old pipeline
twincacca
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8fc869b
since we'll change fastqc, let's leave it like on the template
ctuni
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06d92f1
Merge pull request #71 from ctuni/feature/input_samplesheet
ctuni
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81cd545
Merge pull request #1 from antoine-buetti/add_structure
antoine-buetti
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46cf70c
intergrating fastq_qc_trim_filter_setstrandedness module

Eelco Meerdink
authored and
Eelco Meerdink
committed
71f5f41
added backbone
antoine-buetti
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02d4162
Merge pull request #2 from antoine-buetti/add_structure
antoine-buetti
authored
9e1a084
backbone added 1
antoine-buetti
committed
fb35b9d
Merge pull request #3 from antoine-buetti/add_structure
antoine-buetti
authored
d66a929

Commits on Mar 25, 2025

Delete null/pipeline_info/execution_trace_2025-03-24_11-13-05.txt
ctuni
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087addd
Merge branch 'dev' into dev
ctuni
authored
c962931
removed trailing whitespace
ctuni
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56d42df
first structure for tests
ctuni
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317cbfd
pre-commit checks and comment
ctuni
committed
e4c218b
pre-commit checks and comment
ctuni
committed
f162394
adding the prepare_genome subworkflow
ctuni
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ffbb1f6
adding the prepare_genome subworkflow
ctuni
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c5a2c4f
Merge pull request #80 from ctuni/feature/tests
ctuni
authored
737281c
Merge branch 'dev' into dev
ctuni
authored
092ca9f
Merge branch 'dev' into feature/prepare_genome
ctuni
authored
57051f0
Merge branch 'dev' into dev
ctuni
authored
4791dfd
added new params in schema
ctuni
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41a11ea
Merge branch 'feature/prepare_genome' of https://github.com/ctuni/lncpipe into feature/prepare_genome
ctuni
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0d339d1
Merge pull request #78 from antoine-buetti/dev
ctuni
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daf1751
Merge branch 'dev' into dev
ctuni
authored
d9d8015
Merge branch 'dev' into feature/prepare_genome
ctuni
authored
8b93257
removed a couple of unused tools versions
ctuni
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042795f
Merge branch 'feature/prepare_genome' of https://github.com/ctuni/lncpipe into feature/prepare_genome
ctuni
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ec0918d
intergrating fastq_qc_trim_filter_setstrandedness module

Eelco Meerdink
authored and
Eelco Meerdink
committed
8aa8889
added some lines for pre-procesing

Eelco Meerdink
authored and
Eelco Meerdink
committed
0f15ac1
added correct test profile
ctuni
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4b2c1da
adding missing config options
ctuni
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3de3a9c
added the missing inputs
ctuni
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0b31d79
added the missing inputs
ctuni
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58a815f
added missing script
ctuni
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a88210a
added missing params
ctuni
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3c2a697
fixed ribo_database_manigest
ctuni
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5e657f2
no default it is then
ctuni
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7219cb4
no default it is then
ctuni
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9e1c859
added authors
ctuni
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091e5af
small fix
ctuni
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a61994d
added py script missing
ctuni
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a8aafab
Merge pull request #81 from ctuni/feature/prepare_genome
ctuni
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5abcb97
Merge branch 'dev' into dev
ctuni
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d6440f8
fixing lint
ctuni
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5417b70
params and schema updates
ctuni
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c3cd9dc
Added nf-core stringtie/stringtie, stringtie/merge, star/genomegenerate, bowtie2/align and bowtie2/build modules
Karla Alejandra Ruiz Ceja
committed
e08f673
trying to fix errors
ctuni
committed
3eb265e
fixed includeConfig
ctuni
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e949351
endline
ctuni
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eb1594d
extra params
ctuni
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e048c6f

Commits on Mar 26, 2025

solving everything :cry_emoji:
ctuni
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cccbad4
Merge pull request #79 from Emeerdink/dev
ctuni
authored
6a19de9
Merge branch 'dev' into dev
ctuni
authored
0d240ea
added subworkflows for STAR and HISAT2 copy from nf-core/rnaseq

Eelco Meerdink
authored and
Eelco Meerdink
committed
aa10927
removing bowtie2
ctuni
committed
710712d
fixed json
ctuni
committed
89be599
add all modules for STAR and HISAT2

Eelco Meerdink
authored and
Eelco Meerdink
committed
179df69
updated lncpipe.nf

Eelco Meerdink
authored and
Eelco Meerdink
committed
dd988c3
Merge pull request #82 from karlaarz/dev
ctuni
authored
2b2a188
fixing merge issues

Eelco Meerdink
authored and
Eelco Meerdink
committed
6e30629
Merge branch 'nf-core-dev' into align_dev

Eelco Meerdink
authored and
Eelco Meerdink
committed
bed330f
update nextflow.config and clean lncpipe.nf

Eelco Meerdink
authored and
Eelco Meerdink
committed
4ee7524
added gffcompare module and stringtie subworkflow to lncpipe.nf
Karla Alejandra Ruiz Ceja
committed
1724d8e
add stringtie subworkflow and gffcompare module
Karla Alejandra Ruiz Ceja
committed
3d76fa3
add stringtie subworkflow
Karla Alejandra Ruiz Ceja
committed
54dd3cb
fixing linting
ctuni
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505b312
paths
ctuni
committed
f0f7908
added new star subworkflow
ctuni
committed
3ea217b
Merge branch 'dev' into dev
Emeerdink
authored
cacf53e
a bit of cleanup
ctuni
committed
52a1436
added star as the default aligner for test
ctuni
committed
d9d58dd
removed the view
ctuni
committed
78c1e0a
small change, big effect
ctuni
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7d850e9
linting fastq?
ctuni
committed
d08e663
added proper zcat param for star
ctuni
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d34d470
added missing param
ctuni
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8e10806
schema
ctuni
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abb9ffb
Merge pull request #84 from Emeerdink/align_dev
ctuni
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e55e9ff
Merge branch 'dev' into dev
ctuni
authored
d02e837
linting and cleanup
ctuni
committed
00e5a1d
module cleanup
ctuni
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8fde5d1
module cleanup
ctuni
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051655b
fixing oopsie
ctuni
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a3d44f9
channel factory
ctuni
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b6ec68c
collecting the channel maybe?
ctuni
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f71a519
inputs for gffcompare
ctuni
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61151eb

Commits on Mar 27, 2025

collect the other
ctuni
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4ead56f
trying different things
ctuni
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0f98e17
simplifying
ctuni
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e836d8a
will it work now?
ctuni
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c40dadd
a bit more tinkering
ctuni
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f78f4fe
why is stringtie not runing?
ctuni
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b0a8808
changed name
ctuni
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02bfa57
changed name
ctuni
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5667a7f
adding gffcompare to multiqc
ctuni
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66a71eb
added view to debug
ctuni
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5a443fe
will it work now?
ctuni
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aa3e281
working
ctuni
committed
73a4d4f

Commits on Mar 28, 2025

Merge pull request #85 from karlaarz/dev
Emeerdink
authored
6d9c06e

Commits on Mar 30, 2025

Added subread_featurecounts and htseq modules
Karla Alejandra Ruiz Ceja
committed
52a2d5b

Commits on Apr 2, 2025

Modified some broken pipes
karlaarz
committed
69eee78
Added counts params
karlaarz
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65ede74
Fix indentation issues
karlaarz
committed
d71ebb4
chore: format JSON file with Prettier
karlaarz
committed
64b0f99

Commits on Apr 4, 2025

Merge branch 'dev' into dev
Emeerdink
authored
cc77fdc
Merge pull request #86 from karlaarz/dev
Emeerdink
authored
39e1e23

Commits on Jul 28, 2026

WIP: Remove vulnerable PR-comment artifact pattern

nf-core-bot
authored and
mashehu
committed
51c6184
Merge pull request #88 from nf-core/patch
mashehu
authored
ff1b23f