Implement SPONGE#182

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nictru wants to merge 53 commits intodevfrom

Commits on Jan 16, 2025

removing creation of bindingsite matrix in majority vote

mweyrich28
authored and
nictru
committed
adding sponge for testing

mweyrich28
authored and
nictru
committed
changing process label for circ annotate to medium

mweyrich28
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nictru
committed
passing transcript counts through pipeline to sponge

mweyrich28
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nictru
committed
adding sponge params

mweyrich28
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nictru
committed
adjusting output to match spongeEffects input

mweyrich28
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nictru
committed
adding sponge effects for testing

mweyrich28
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nictru
committed
solving version conflict in container

mweyrich28
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nictru
committed
removing deseq2 norm from sponge template

mweyrich28
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nictru
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adding additional deseq2 normalization process for tx counts

mweyrich28
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nictru
committed
removing pacman call in sponge_effects

mweyrich28
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nictru
committed
updating sponge_effects container to include gsva

mweyrich28
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nictru
committed
adding and renaming deseq2_normalisation processes

mweyrich28
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nictru
committed
removing redundant param

mweyrich28
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nictru
committed
fixing input for tx_normalization

mweyrich28
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nictru
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adding versions file to R script of tx_normalization

mweyrich28
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nictru
committed
formatting

mweyrich28
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nictru
committed
adding versions to output of sponge effects

mweyrich28
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nictru
committed
adding tarpmir module

mweyrich28
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nictru
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including tarpmir unification in binding site prediction

mweyrich28
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nictru
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adding tarpmir as tool in nf config

mweyrich28
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nictru
committed
grouping mirna options together

mweyrich28
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nictru
committed
fixing python version in majority_vote

mweyrich28
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nictru
committed
adding main pita process

mweyrich28
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nictru
committed
adding adjusted pita template

mweyrich28
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nictru
committed
typo

mweyrich28
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nictru
committed
adding config for pita and adjusting config for tarpmir

mweyrich28
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nictru
committed
adding pita libs and Bin

mweyrich28
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nictru
committed
removing artifact in sponge.R

mweyrich28
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nictru
committed
adding tarpmir process

mweyrich28
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nictru
committed
ordering imports

mweyrich28
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nictru
committed
adding pita and tarpmir to tool selection

mweyrich28
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nictru
committed
reformatting

mweyrich28
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nictru
committed
adding SPONGE_EFFECTS versions

mweyrich28
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nictru
committed
adding pita in mirna_prediction for testing

mweyrich28
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nictru
committed
adding pita params

mweyrich28
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nictru
committed
adding tarpmir params

mweyrich28
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nictru
committed
adding missing ;

mweyrich28
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nictru
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fixing output of pita

mweyrich28
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nictru
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adding versios.yml for pita_predict

mweyrich28
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nictru
committed
adding unify pita in conf

mweyrich28
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nictru
committed
adding pita to mirna_bindingsites subworkflow

mweyrich28
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nictru
committed
formatting

mweyrich28
authored and
nictru
committed
adjusting mirna tool filter param

mweyrich28
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nictru
committed
removing outdated params

mweyrich28
authored and
nictru
committed
Latest changes from Malte
nictru
committed
Re-enable everything in mirna_bindingsites subworkflow
nictru
committed
Improve mirna majority vote script
nictru
committed
Improve SPONGE script
nictru
committed
Re-enable commented-out sections from mirna prediction
nictru
committed

Commits on Jan 19, 2025