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Improve circRNA-miRNA interaction analysis #166

Merged
merged 80 commits into from
Aug 8, 2024
Merged

Improve circRNA-miRNA interaction analysis #166

merged 80 commits into from
Aug 8, 2024

Commits on Aug 6, 2024

  1. Adding mirna_expression param to subworkflow mirna_prediction

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  2. Adding mirna_expression param to config

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  3. Adding mirna_expression param to nextflow_schema.json

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  4. adding process DESEQ2_NORMALIZATION

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    Malte Weyrich authored and nictru committed Aug 6, 2024
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  5. Adding deseq2 module and mirna normalization module (including params)

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    Malte Weyrich authored and nictru committed Aug 6, 2024
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  6. Adding formatting of mirna prediction output

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    Malte Weyrich authored and nictru committed Aug 6, 2024
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  7. embedding mirna filtering and output formatting in mirna_prediction s… 

    …ubworkflow
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    Malte Weyrich authored and nictru committed Aug 6, 2024
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  8. extending miranda output formatting to ignore unwanted prefix

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    Malte Weyrich authored and nictru committed Aug 6, 2024
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  9. implementing concatenation of mirna predictions, work in progress

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  10. preparing majority vote

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  11. fixing channel structure of predictions for cat cat

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    Malte Weyrich authored and nictru committed Aug 6, 2024
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  12. Embedding majority vote for mirna predictions

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  13. updating miranda to majority gawk

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  14. adding compute correlations module

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  15. todos

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  16. Replace tabs with spaces

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  17. Implement MIRNA_BINDINGSITES subworkflow

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  18. Add versions capture for MIRNA_BINDINGSITES

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  19. Use full transcriptome in miRNA binding site detection

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  20. Use BIOAWK for ADD_BACKSPLICE

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  21. Pass correct count info to mirna_prediction

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  22. Implement transcriptome batch splitting in MIRNA_BINDINGSITES

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  23. Improve targetscan input preparation

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  24. Improve majority vote script

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  25. Improve styling

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  26. Add majority targets output

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  27. Transpose binding site output

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  28. Start refactoring correlation

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  29. Implement first draft of correlation analysis

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  30. Save correlation results

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  31. Switch correlation output to TSV

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  32. Handle correlation output channels

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  33. fixing MIRNA_TARGETS

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  34. Filtering mature based on filtered mirnas

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  35. Adding missing .collect() to MIRANDA process

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  36. fixing filtering of mature

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  37. Cleaning up

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  38. Adding param to switch between spearman and pearson correlation

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  39. More resources for MAJORITY_VOTE

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  40. removing todo comment

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  41. removing TODO comment

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  42. correlations output set to optional

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  43. Fix major rebase problems

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  44. Fix small bug with backsplice junction adding

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  45. Improve mirna prediction formatting

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  46. Improve output structure for mirna prediction

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  47. fixing formatting in modules

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  48. adjusting mirna_min_reads to match nextflow_schema

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

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

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  51. updating nf-core modules

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  52. Revert "updating nf-core modules" 

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

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  54. 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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  6. making mirna_expression parameter optional

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  7. Apply suggestions from code review 

    Co-authored-by: Nico Trummer <[email protected]>
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  8. renaming mirna_vote to mirna_tool_filter

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Commits on Aug 8, 2024

  1. applying prettier

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  2. renaming mirna_tools in nextflow.config

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  3. fixing indent

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  4. deleting redundant file

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  5. rewording usage

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  6. rewording usage

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  7. reformatting compute correlations

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  8. reformatting normalization

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  9. reformatting majority vote

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  10. reformatting majority vote py

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  11. reformatting mirna filtering R

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  12. reformatting mirna bindingsites

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  13. reformatting mirna prediction

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  14. fixing param mirna_tool_filter

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  15. checking if mirna_expression is null before passing it to file()

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  16. Apply suggestions from code review 

    Co-authored-by: Nico Trummer <[email protected]>
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  17. applying correct format to mirna_tools

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  18. updating default format of mirna_tools

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