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Implement SPONGE #182

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Implement SPONGE #182

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@nictru nictru commented Jan 19, 2025

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@mweyrich28 @nictru
removing creation of bindingsite matrix in majority vote
96863f2
@mweyrich28 @nictru
adding sponge for testing
a82d1f9
@mweyrich28 @nictru
changing process label for circ annotate to medium
0548d99
@mweyrich28 @nictru
passing transcript counts through pipeline to sponge
6fb5a6e
@mweyrich28 @nictru
adding sponge params
24f139b
@mweyrich28 @nictru
adjusting output to match spongeEffects input
e987ac1
@mweyrich28 @nictru
adding sponge effects for testing
77b52dc
@mweyrich28 @nictru
solving version conflict in container
e2aa28e
@mweyrich28 @nictru
removing deseq2 norm from sponge template
50628d5
@mweyrich28 @nictru
adding additional deseq2 normalization process for tx counts
d9144a3
@mweyrich28 @nictru
removing pacman call in sponge_effects
ae37fb8
@mweyrich28 @nictru
updating sponge_effects container to include gsva
20f8609
@mweyrich28 @nictru
adding and renaming deseq2_normalisation processes
656c76e
@mweyrich28 @nictru
removing redundant param
79bd298
@mweyrich28 @nictru
fixing input for tx_normalization
d44046f
@mweyrich28 @nictru
adding versions file to R script of tx_normalization
8d685db
@mweyrich28 @nictru
formatting
aa2db97
@mweyrich28 @nictru
adding versions to output of sponge effects
b04afc6
@mweyrich28 @nictru
adding tarpmir module
cb7f82f
@mweyrich28 @nictru
including tarpmir unification in binding site prediction
9e9d380
@mweyrich28 @nictru
adding tarpmir as tool in nf config
c2c64cf
@mweyrich28 @nictru
grouping mirna options together
f3aeba7
@mweyrich28 @nictru
fixing python version in majority_vote
494dca3
@mweyrich28 @nictru
adding main pita process
a7e0655
@mweyrich28 @nictru
adding adjusted pita template
41d4413
@mweyrich28 @nictru
typo
b7c9ea2
@mweyrich28 @nictru
adding config for pita and adjusting config for tarpmir
e321dc8
@mweyrich28 @nictru
adding pita libs and Bin
d57f234
@mweyrich28 @nictru
removing artifact in sponge.R
41f29de
@mweyrich28 @nictru
adding tarpmir process
1731391
mweyrich28 and others added 23 commits January 16, 2025 11:28
@mweyrich28 @nictru
ordering imports
b0fb25b
@mweyrich28 @nictru
adding pita and tarpmir to tool selection
25e71a8
@mweyrich28 @nictru
reformatting
1373e39
@mweyrich28 @nictru
adding SPONGE_EFFECTS versions
e484058
@mweyrich28 @nictru
adding pita in mirna_prediction for testing
7646471
@mweyrich28 @nictru
adding pita params
c07f510
@mweyrich28 @nictru
adding tarpmir params
ad001a4
@mweyrich28 @nictru
adding missing ;
3c4acc9
@mweyrich28 @nictru
fixing output of pita
533af26
@mweyrich28 @nictru
adding versios.yml for pita_predict
f79c6f4
@mweyrich28 @nictru
adding unify pita in conf
f7141df
@mweyrich28 @nictru
adding pita to mirna_bindingsites subworkflow
8412b1c
@mweyrich28 @nictru
formatting
8d0b8f2
@mweyrich28 @nictru
adjusting mirna tool filter param
09b4d7e
@mweyrich28 @nictru
removing outdated params
cb2afba
@nictru
Latest changes from Malte
2e66b06
@nictru
Re-enable everything in mirna_bindingsites subworkflow
d1525e7
@nictru
Improve mirna majority vote script
2075095
@nictru
Improve SPONGE script
bc7b7de
@nictru
Re-enable commented-out sections from mirna prediction
705f2f4
@nictru
Improve mirna module structure
7b93466
@nictru
Add note on SPONGE execution
c4b52a2
@nictru
Make ciriquant_de output optional
5a35f99
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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3 participants
@nictru @nf-core-bot @mweyrich28