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Implement SPONGE#182

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nictru wants to merge 53 commits intodevnf-core/circrna:devfrom spongingnf-core/circrna:spongingCopy head branch name to clipboard

+232,870-57

Commits

Commits on Jan 16, 2025

• removing creation of bindingsite matrix in majority vote

  

  mweyrich28

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  nictru

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  96863f2

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• adding sponge for testing

  

  mweyrich28

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  nictru

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  a82d1f9

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• changing process label for circ annotate to medium

  

  mweyrich28

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  0548d99

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• passing transcript counts through pipeline to sponge

  

  mweyrich28

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  nictru

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  6fb5a6e

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• adding sponge params

  

  mweyrich28

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  24f139b

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• adjusting output to match spongeEffects input

  

  mweyrich28

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  e987ac1

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• adding sponge effects for testing

  

  mweyrich28

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  77b52dc

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• solving version conflict in container

  

  mweyrich28

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  e2aa28e

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• removing deseq2 norm from sponge template

  

  mweyrich28

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  50628d5

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• adding additional deseq2 normalization process for tx counts

  

  mweyrich28

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  d9144a3

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• removing pacman call in sponge_effects

  

  mweyrich28

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  nictru

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  ae37fb8

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• updating sponge_effects container to include gsva

  

  mweyrich28

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  20f8609

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• adding and renaming deseq2_normalisation processes

  

  mweyrich28

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  656c76e

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• removing redundant param

  

  mweyrich28

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  79bd298

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• fixing input for tx_normalization

  

  mweyrich28

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• adding versions file to R script of tx_normalization

  

  mweyrich28

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  8d685db

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• formatting

  

  mweyrich28

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  aa2db97

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• adding versions to output of sponge effects

  

  mweyrich28

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  b04afc6

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• adding tarpmir module

  

  mweyrich28

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• including tarpmir unification in binding site prediction

  

  mweyrich28

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  9e9d380

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• adding tarpmir as tool in nf config

  

  mweyrich28

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• grouping mirna options together

  

  mweyrich28

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  f3aeba7

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• fixing python version in majority_vote

  

  mweyrich28

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  494dca3

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• adding main pita process

  

  mweyrich28

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  a7e0655

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• adding adjusted pita template

  

  mweyrich28

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  41d4413

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• typo

  

  mweyrich28

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  b7c9ea2

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• adding config for pita and adjusting config for tarpmir

  

  mweyrich28

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  e321dc8

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• adding pita libs and Bin

  

  mweyrich28

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  d57f234

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• removing artifact in sponge.R

  

  mweyrich28

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  41f29de

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• adding tarpmir process

  

  mweyrich28

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• ordering imports

  

  mweyrich28

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  b0fb25b

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• adding pita and tarpmir to tool selection

  

  mweyrich28

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  nictru

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  25e71a8

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• reformatting

  

  mweyrich28

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  1373e39

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• adding SPONGE_EFFECTS versions

  

  mweyrich28

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  e484058

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• adding pita in mirna_prediction for testing

  

  mweyrich28

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  7646471

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• adding pita params

  

  mweyrich28

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  c07f510

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• adding tarpmir params

  

  mweyrich28

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  ad001a4

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• adding missing ;

  

  mweyrich28

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  3c4acc9

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• fixing output of pita

  

  mweyrich28

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  533af26

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• adding versios.yml for pita_predict

  

  mweyrich28

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  f79c6f4

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• adding unify pita in conf

  

  mweyrich28

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  f7141df

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• adding pita to mirna_bindingsites subworkflow

  

  mweyrich28

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• formatting

  

  mweyrich28

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  8d0b8f2

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• adjusting mirna tool filter param

  

  mweyrich28

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  09b4d7e

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• removing outdated params

  

  mweyrich28

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  cb2afba

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• Latest changes from Malte

  nictru

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• Re-enable everything in mirna_bindingsites subworkflow

  nictru

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• Improve mirna majority vote script

  nictru

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• Improve SPONGE script

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  bc7b7de

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• Re-enable commented-out sections from mirna prediction

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Commits on Jan 19, 2025

• Improve mirna module structure

  nictru

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  7b93466

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• Add note on SPONGE execution

  nictru

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  c4b52a2

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• Make ciriquant_de output optional

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