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[Do not merge!] Pseudo PR for first release #69

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[Do not merge!] Pseudo PR for first release #69

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Commits on May 30, 2024

  1. Update nf-core modules

    @nictru
    nictru committed May 30, 2024
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  2. Update segemehl unify call

    @nictru
    nictru committed May 30, 2024
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  3. Merge pull request #123 from nf-core/segemehl-update 

    Segemehl update
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    nictru committed May 30, 2024
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Commits on May 31, 2024

  1. Add support for ext.args in ciriquant

    @nictru
    nictru committed May 31, 2024
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  2. Merge pull request #124 from nf-core/ciriquant-args 

    Add support for ext.args in ciriquant
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    nictru committed May 31, 2024
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  3. Add strandedness to samplesheet

    @nictru
    nictru committed May 31, 2024
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  4. Add support for strandedness in ciriquant

    @nictru
    nictru committed May 31, 2024
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  5. Revise DCC parameters

    @nictru
    nictru committed May 31, 2024
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  6. Implement ext.args interface for find_circ

    @nictru
    nictru committed May 31, 2024
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  7. Fix trimming indentation in modules.config

    @nictru
    nictru committed May 31, 2024
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  8. Move segemehl index location in modules.config

    @nictru
    nictru committed May 31, 2024
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  9. Add strandedness to bowtie2 calls

    @nictru
    nictru committed May 31, 2024
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  10. Add strandedness to find_circ

    @nictru
    nictru committed May 31, 2024
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Commits on Jun 9, 2024

  1. Add strandedness documentation

    @nictru
    nictru committed Jun 9, 2024
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  2. Add samplesheet validation for strandedness of runs of the same sample

    @nictru
    nictru committed Jun 9, 2024
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  3. Update modules

    @nictru
    nictru committed Jun 9, 2024
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  4. Merge pull request #132 from nf-core/module-updates_24-06 

    Update modules
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    nictru committed Jun 9, 2024
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Commits on Jun 10, 2024

  1. Merge pull request #131 from nf-core/strandedness 

    Add support for setting strandedness in samplesheet
    @nictru
    nictru committed Jun 10, 2024
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  2. Add new STATISTICAL_TESTS subworkflow

    @nictru
    nictru committed Jun 10, 2024
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  3. Implement CIRCTEST_PREPARE

    @nictru
    nictru committed Jun 10, 2024
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Commits on Jun 11, 2024

  1. Implement circTest

    @nictru
    nictru committed Jun 11, 2024
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  2. Fix circtest problems

    @nictru
    nictru committed Jun 11, 2024
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  3. Re-enable circtest plots

    @nictru
    nictru committed Jun 11, 2024
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  4. Fix circtest plot problem

    @nictru
    nictru committed Jun 11, 2024
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  5. Remove artifacts of old differential expression analysis

    @nictru
    nictru committed Jun 11, 2024
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  6. Simplify annotation module

    @nictru
    nictru committed Jun 11, 2024
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  7. Switch annotation to template syntax

    @nictru
    nictru committed Jun 11, 2024
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  8. Remove unused combine_quantification script

    @nictru
    nictru committed Jun 11, 2024
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  9. Switch merge_samples to template syntax

    @nictru
    nictru committed Jun 11, 2024
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  10. Switch to template syntax in merge_tools

    @nictru
    nictru committed Jun 11, 2024
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  11. Remove custom DESeq2 module

    @nictru
    nictru committed Jun 11, 2024
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  12. Remove DIFFERENTIAL_EXPRESSION traces

    @nictru
    nictru committed Jun 11, 2024
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  13. Remove unwanted biotypes

    @nictru
    nictru committed Jun 11, 2024
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  14. Fix linting problems

    @nictru
    nictru committed Jun 11, 2024
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  15. Prettier

    @nictru
    nictru committed Jun 11, 2024
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Commits on Jun 12, 2024

  1. Remove traces of differential_expression in docs

    @nictru
    nictru committed Jun 12, 2024
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Commits on Jun 14, 2024

  1. Update modules/local/circtest/circtest/main.nf 

    Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
    @nictru @mahesh-panchal
    nictru and mahesh-panchal committed Jun 14, 2024
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  2. Clarify docs

    @nictru
    nictru committed Jun 14, 2024
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  3. Update gnu/sort

    @nictru
    nictru committed Jun 14, 2024
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  4. Merge pull request #147 from nf-core/144-differential-expression 

    Clean up differential expression workflow
    @nictru
    nictru committed Jun 14, 2024
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  5. Change conditions for downstream tasks

    @nictru
    Diana Bassow authored and nictru committed Jun 14, 2024
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  6. Changed documentation 'phenotype' and 'mature'

    @nictru
    Diana Bassow authored and nictru committed Jun 14, 2024
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  7. Remove module traces of module parameter

    @nictru
    nictru committed Jun 14, 2024
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  8. Fix nextflow_schema.json

    @nictru
    nictru committed Jun 14, 2024
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  9. Make phenotype optional for quantification

    @nictru
    nictru committed Jun 14, 2024
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  10. Improve documentation of the phenotype parameter

    @nictru
    nictru committed Jun 14, 2024
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  11. Update documentation for enabling miRNA prediction

    @nictru
    nictru committed Jun 14, 2024
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  12. Update README

    @nictru
    nictru committed Jun 14, 2024
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  13. Update usage documentation to follow rnaseq example

    @nictru
    nictru committed Jun 14, 2024
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  14. Update nextflow schema order

    @nictru
    nictru committed Jun 14, 2024
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  15. Update ouput docs

    @nictru
    nictru committed Jun 14, 2024
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  16. Prettier

    @nictru
    nictru committed Jun 14, 2024
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Commits on Jun 15, 2024

  1. Merge pull request #148 from nf-core/deprecate_module 

    Deprecate module parameter
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    nictru committed Jun 15, 2024
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Commits on Jun 17, 2024

  1. Add annotations parameter and pass it to the according position

    @nictru
    nictru committed Jun 17, 2024
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  2. Make annotations parameter optional

    @nictru
    nictru committed Jun 17, 2024
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  3. Unify annotation naming

    @nictru
    nictru committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. First database annotation implementation

    @nictru
    nictru committed Jun 18, 2024
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  2. Fix per-sample DB annotation

    @nictru
    nictru committed Jun 18, 2024
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  3. Change database intersection strategy

    @nictru
    nictru committed Jun 18, 2024
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  4. Make sure databases are optional

    @nictru
    nictru committed Jun 18, 2024
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  5. Add db annotation to annotation python script

    @nictru
    nictru committed Jun 18, 2024
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  6. Fix first row length bug

    @nictru
    nictru committed Jun 18, 2024
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  7. Make sure annotation input is optional

    @nictru
    nictru committed Jun 18, 2024
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  8. Merge pull request #149 from nf-core/138-implement-circrna-database-a… 

    …nnotation-functionalities

Implement circrna database annotation functionalities
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    nictru committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. Use psirc bioconda package

    @nictru
    nictru committed Jun 19, 2024
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  2. Escape problematic $

    @nictru
    nictru committed Jun 19, 2024
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  3. Fix problematic $ also in psirc index

    @nictru
    nictru committed Jun 19, 2024
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  4. Merge pull request #152 from nf-core/115-add-bioconda-recipe-for-psirc 

    Use psirc bioconda package
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    nictru committed Jun 19, 2024
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Commits on Jun 23, 2024

  1. Implement GTF filtering

    @nictru
    nictru committed Jun 23, 2024
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  2. Escape backslashes

    @nictru
    nictru committed Jun 23, 2024
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Commits on Jun 24, 2024

  1. Fix pandas references

    @nictru
    nictru committed Jun 24, 2024
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  2. Remove problematic r-base singularity image

    @nictru
    nictru committed Jun 24, 2024
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  3. Add missing environment yml files

    @nictru
    nictru committed Jun 24, 2024
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  4. Add another missing environment yml

    @nictru
    nictru committed Jun 24, 2024
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Commits on Jun 25, 2024

  1. Add tximeta environment.yml

    @nictru
    nictru committed Jun 25, 2024
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  2. Fix GTF sorting

    @nictru
    nictru committed Jun 25, 2024
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  3. Fix typo on merge_experiments conda environment

    @nictru
    nictru committed Jun 25, 2024
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  4. Fix merge_experiments environment definition

    @nictru
    nictru committed Jun 25, 2024
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  5. Fix typo

    @nictru
    nictru committed Jun 25, 2024
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  6. Merge pull request #153 from nf-core/conda-envs 

    Conda envs
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    nictru committed Jun 25, 2024
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Commits on Jun 27, 2024

  1. Fix circexplorer2 count location

    @nictru
    nictru committed Jun 27, 2024
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  2. Merge pull request #154 from nf-core/circexplorer2-counts 

    Fix circexplorer2 count location
    @nictru
    nictru committed Jun 27, 2024
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Commits on Jul 15, 2024

  1. Use nf core module for gtffilter functionality

    @nictru
    nictru committed Jul 15, 2024
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  2. Rename GTFFILTER module accession

    @nictru
    nictru committed Jul 15, 2024
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  3. Update GTFFILTER module

    @nictru
    nictru committed Jul 15, 2024
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  4. Merge pull request #157 from nf-core/151-error-no-genomic-sequence-av… 

    …ailable-check-g-option-error-in-gffread-command-for-task-nfcore_circrnacircrnaquantificationtranscriptome-error

Remove GTF regions on unknown chromosomes
    @nictru
    nictru committed Jul 15, 2024
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Commits on Aug 1, 2024

  1. Add filter for circular RNAs to find_circ

    @nictru
    nictru committed Aug 1, 2024
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  2. Update comment

    @nictru
    nictru committed Aug 1, 2024
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  3. Merge pull request #165 from nf-core/find_circ_bug 

    Add filter for circular RNAs to find_circ
    @nictru
    nictru committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. Add error message for empty intersections

    @nictru
    nictru committed Aug 2, 2024
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  2. Add docs for GTF required attributes

    @nictru
    nictru committed Aug 2, 2024
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  3. Add check for presence of attributes in annotation intersection

    @nictru
    nictru committed Aug 2, 2024
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  4. Fix bug in missing attribute check

    @nictru
    nictru committed Aug 2, 2024
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  5. Implement Segemehl grouping

    @nictru
    nictru committed Aug 2, 2024
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  6. Add bedtools groupby

    @nictru
    nictru committed Aug 2, 2024
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  7. Fix segemehl grouping

    @nictru
    nictru committed Aug 2, 2024
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  8. Implement ordering of segemehl results

    @nictru
    nictru committed Aug 2, 2024
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  9. Implement check for duplicates in tool results

    @nictru
    nictru committed Aug 2, 2024
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  10. Implement custom BSJome generation

    @nictru
    nictru committed Aug 2, 2024
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  11. Extract annotation from discovery

    @nictru
    nictru committed Aug 2, 2024
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  12. Fix bug in tool filtering

    @nictru
    nictru committed Aug 2, 2024
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  13. Fix saveAs conditions

    @nictru
    nictru committed Aug 2, 2024
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  14. Fix some output definitions

    @nictru
    nictru committed Aug 2, 2024
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  15. Add per-sample and combined output directories for discovery

    @nictru
    nictru committed Aug 2, 2024
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  16. Add tools subdirectory to discovery outdir

    @nictru
    nictru committed Aug 2, 2024
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  17. Implement separate processes for FASTA extraction

    @nictru
    nictru committed Aug 2, 2024
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  18. Add fastas to discovery output

    @nictru
    nictru committed Aug 2, 2024
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  19. Add output directory for statistical tests

    @nictru
    nictru committed Aug 2, 2024
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  20. Handle output of circtest_prepare

    @nictru
    nictru committed Aug 2, 2024
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  21. Improve QC output directory structure

    @nictru
    nictru committed Aug 2, 2024
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  22. Unify discovery tool output directories

    @nictru
    nictru committed Aug 2, 2024
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  23. Improve quantification outdir structure

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  24. Improve quantification outdir structure

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  25. Make some more outdir optimizations

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  26. Remove tool reference in mirna outdir

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  27. Add annotation back to discovery

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  28. Improve annotation output formatting

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  29. Remove unnecessary outputs from circrna_discovery

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  30. Fix bug in tool filtering

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  31. Prevent pipeline from failing if no circRNAs are found

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Commits on Aug 3, 2024

  1. Improve annotation output format

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  2. Remove traces of old merging functionality

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  3. Make sure pipeline fails in an ordered way if no circRNAs are found

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  4. Improve error message for no circRNAs found

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  5. Linting

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  6. Update first section of introduction

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  7. Update credits

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  8. Restructure usage docs

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  9. Add plans for future implementations to README

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  10. Rename CIRCRNA_DISCOVERY to BSJ_DETECTION

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  11. Rename params.tool to params.tools

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  12. Remove unused species_id parameter

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  13. Apply parameter changes to test configs

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  14. Change some default values

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  15. Finish updating usage docs

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  16. Add output directory structure documentation

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  17. Add documentation for references output

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  18. Improve STAR output documentation

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  19. Improve output docs for various detection tools

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  20. Finalize BSJ detection output docs

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  21. Update output docs for mirna prediction and quantification

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  22. Prettier

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Commits on Aug 6, 2024

  1. Update README.md 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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  2. Update README.md 

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  3. Update docs/output.md 

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  4. Update docs/output.md 

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  5. Update nextflow_schema.json 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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  6. Update nextflow_schema.json 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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  7. Update docs/output.md 

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  8. Update docs/output.md 

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  9. Update docs/usage.md 

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  10. Update docs/usage.md 

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  11. Update docs/output.md 

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  12. Update docs/output.md 

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  13. Update docs/output.md 

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  14. Update docs/output.md 

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  15. Fix syntax error in nextflow_schema.json

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  16. Write pipeline name in standard formatting in output docs

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  17. Update bsj_reads help text

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  18. Merge pull request #159 from nf-core/150-problems-with-empty-annotati… 

    …on-intersection

Fix problems with empty annotation intersection
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  19. Adding mirna_expression param to subworkflow mirna_prediction

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  20. Adding mirna_expression param to config

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  21. Adding mirna_expression param to nextflow_schema.json

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  22. adding process DESEQ2_NORMALIZATION

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  23. Adding deseq2 module and mirna normalization module (including params)

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  24. Adding formatting of mirna prediction output

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  25. embedding mirna filtering and output formatting in mirna_prediction s… 

    …ubworkflow
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  26. extending miranda output formatting to ignore unwanted prefix

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  27. implementing concatenation of mirna predictions, work in progress

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  28. preparing majority vote

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  29. fixing channel structure of predictions for cat cat

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  30. Embedding majority vote for mirna predictions

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  31. updating miranda to majority gawk

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  32. adding compute correlations module

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  33. todos

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  34. Replace tabs with spaces

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  35. Implement MIRNA_BINDINGSITES subworkflow

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  36. Add versions capture for MIRNA_BINDINGSITES

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  37. Use full transcriptome in miRNA binding site detection

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  38. Use BIOAWK for ADD_BACKSPLICE

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  39. Pass correct count info to mirna_prediction

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  40. Implement transcriptome batch splitting in MIRNA_BINDINGSITES

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  41. Improve targetscan input preparation

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  42. Improve majority vote script

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  43. Improve styling

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  44. Add majority targets output

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  45. Transpose binding site output

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  46. Start refactoring correlation

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  47. Implement first draft of correlation analysis

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  48. Save correlation results

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  49. Switch correlation output to TSV

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  50. Handle correlation output channels

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  51. fixing MIRNA_TARGETS

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  52. Filtering mature based on filtered mirnas

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  53. Adding missing .collect() to MIRANDA process

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  54. fixing filtering of mature

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  55. Cleaning up

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  56. Adding param to switch between spearman and pearson correlation

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  57. More resources for MAJORITY_VOTE

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  58. removing todo comment

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  59. removing TODO comment

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  60. correlations output set to optional

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  61. Fix major rebase problems

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  62. Fix small bug with backsplice junction adding

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  63. Improve mirna prediction formatting

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  64. Improve output structure for mirna prediction

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  65. fixing formatting in modules

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  66. adjusting mirna_min_reads to match nextflow_schema

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  67. fixing formatting and adding missing allOf field for mirna_processing… 

    …_options
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  68. removing non used configs in modules.config

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  69. updating nf-core modules

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  70. Revert "updating nf-core modules" 

    This reverts commit 4cbb345.
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  71. only updating necessary modules

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  72. fixing pattern for input file of mirna_expression

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Commits on Aug 7, 2024

  1. Adding missing html tag in output.md

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  2. updating output.md in docs 

    Updating the mirna_prediction section
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  3. capitalizing 'tsv' to TSV

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  4. updating usage.md

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  5. updating README.md

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    mweyrich28 committed Aug 7, 2024
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  6. making mirna_expression parameter optional

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    mweyrich28 committed Aug 7, 2024
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  7. Apply suggestions from code review 

    Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>
    @mweyrich28 @nictru
    mweyrich28 and nictru committed Aug 7, 2024
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  8. renaming mirna_vote to mirna_tool_filter

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    mweyrich28 committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. applying prettier

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    mweyrich28 committed Aug 8, 2024
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  2. renaming mirna_tools in nextflow.config

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    mweyrich28 committed Aug 8, 2024
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  3. fixing indent

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    mweyrich28 committed Aug 8, 2024
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  4. deleting redundant file

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    mweyrich28 committed Aug 8, 2024
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  5. rewording usage

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    mweyrich28 committed Aug 8, 2024
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  6. rewording usage

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    mweyrich28 committed Aug 8, 2024
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  7. reformatting compute correlations

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    mweyrich28 committed Aug 8, 2024
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  8. reformatting normalization

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    mweyrich28 committed Aug 8, 2024
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  9. reformatting majority vote

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    mweyrich28 committed Aug 8, 2024
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  10. reformatting majority vote py

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    mweyrich28 committed Aug 8, 2024
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  11. reformatting mirna filtering R

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    mweyrich28 committed Aug 8, 2024
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  12. reformatting mirna bindingsites

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    mweyrich28 committed Aug 8, 2024
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  13. reformatting mirna prediction

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    mweyrich28 committed Aug 8, 2024
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  14. fixing param mirna_tool_filter

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    mweyrich28 committed Aug 8, 2024
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  15. checking if mirna_expression is null before passing it to file()

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    mweyrich28 committed Aug 8, 2024
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  16. Apply suggestions from code review 

    Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>
    @mweyrich28 @nictru
    mweyrich28 and nictru committed Aug 8, 2024
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  17. applying correct format to mirna_tools

    @mweyrich28
    mweyrich28 committed Aug 8, 2024
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  18. updating default format of mirna_tools

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    mweyrich28 committed Aug 8, 2024
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  19. Merge pull request #166 from nf-core/sponging 

    Improve circRNA-miRNA interaction analysis
    @mweyrich28
    mweyrich28 committed Aug 8, 2024
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  20. Add credits for mweyrich

    @nictru
    nictru committed Aug 8, 2024
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  21. Merge pull request #167 from nf-core/credits-mweyrich 

    Add credits for mweyrich
    @nictru
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  22. Implement count extraction

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    nictru committed Aug 8, 2024
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  23. Implement per-tool count combination across samples

    @nictru
    nictru committed Aug 8, 2024
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  24. Restructure BSJ detection workflow

    @nictru
    nictru committed Aug 8, 2024
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  25. Update docs

    @nictru
    nictru committed Aug 8, 2024
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  26. Perform outer join on counts

    @nictru
    nictru committed Aug 8, 2024
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  27. Imporve BSJ_DETECTION order

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    nictru committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Merge pull request #168 from nf-core/per-tool-quantification 

    Add output containing per-tool quantification
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    nictru committed Aug 9, 2024
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