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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 Aug 1, 2024

  1. Update comment

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  2. Merge pull request #165 from nf-core/find_circ_bug 

    Add filter for circular RNAs to find_circ
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Commits on Aug 2, 2024

  1. Add error message for empty intersections

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  2. Add docs for GTF required attributes

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  3. Add check for presence of attributes in annotation intersection

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  4. Fix bug in missing attribute check

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  5. Implement Segemehl grouping

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  6. Add bedtools groupby

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  7. Fix segemehl grouping

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  8. Implement ordering of segemehl results

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  9. Implement check for duplicates in tool results

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  10. Implement custom BSJome generation

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  11. Extract annotation from discovery

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  12. Fix bug in tool filtering

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  13. Fix saveAs conditions

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  14. Fix some output definitions

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  15. Add per-sample and combined output directories for discovery

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  16. Add tools subdirectory to discovery outdir

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  17. Implement separate processes for FASTA extraction

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  18. Add fastas to discovery output

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  19. Add output directory for statistical tests

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  20. Handle output of circtest_prepare

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  21. Improve QC output directory structure

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  22. Unify discovery tool output directories

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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

    @nictru
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  2. Remove traces of old merging functionality

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

    @nictru
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  4. Improve error message for no circRNAs found

    @nictru
    nictru committed Aug 3, 2024
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  5. Linting

    @nictru
    nictru committed Aug 3, 2024
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  6. Update first section of introduction

    @nictru
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  7. Update credits

    @nictru
    nictru committed Aug 3, 2024
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  8. Restructure usage docs

    @nictru
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  9. Add plans for future implementations to README

    @nictru
    nictru committed Aug 3, 2024
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  10. Rename CIRCRNA_DISCOVERY to BSJ_DETECTION

    @nictru
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  11. Rename params.tool to params.tools

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  12. Remove unused species_id parameter

    @nictru
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  13. Apply parameter changes to test configs

    @nictru
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  14. Change some default values

    @nictru
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  15. Finish updating usage docs

    @nictru
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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 <[email protected]>
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  2. Update README.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  3. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  4. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  5. Update nextflow_schema.json 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  6. Update nextflow_schema.json 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  7. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  8. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  9. Update docs/usage.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  10. Update docs/usage.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  11. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  12. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  13. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  14. Update docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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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

    @mweyrich28 @nictru
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  52. Filtering mature based on filtered mirnas

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  53. Adding missing .collect() to MIRANDA process

    @mweyrich28 @nictru
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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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  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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  19. Merge pull request #166 from nf-core/sponging 

    Improve circRNA-miRNA interaction analysis
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  20. Add credits for mweyrich

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  21. Merge pull request #167 from nf-core/credits-mweyrich 

    Add credits for mweyrich
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  22. Implement count extraction

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  23. Implement per-tool count combination across samples

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  24. Restructure BSJ detection workflow

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  25. Update docs

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  26. Perform outer join on counts

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  27. Imporve BSJ_DETECTION order

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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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Commits on Aug 23, 2024

  1. Simplify ciriquant config creation

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  2. Implement support for single-stranded libraries

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  3. Add support for bed files in ciriquant

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  4. Add support for multiple quantification methods

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  5. Implement first bit of global ciriquant quantification

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  6. Enable ciriquant gene quantification

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Commits on Aug 24, 2024

  1. Implement ciriquant circ count extraction

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  2. Generalize gffread module

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  3. Further generalize gffread

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  4. Improve gffread fasta creation

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  5. Use nf-core gffread module and add pygtftk

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  6. Implement gene expression extraction

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  7. Implement ciriquant expression column naming

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  8. Implement ciriquant expression joining

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  9. Improve ciriquant handling

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  10. Implement channel handling for ciriquant DEA

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  11. Implement ciriquant_dea samplesheet creation

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  12. Implement ciriquant DEA preprocessing

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  13. Implement capturing of stringtie results from ciriquant

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  14. Implement basic stringtie_prepde

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  15. Switch back to official ciriquant image to prevent stringtie compatib… 

    …ility problems
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  16. Rename ciriquant DE preparation module

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  17. Implement ciriquant de analysis

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  18. Improve ciriquant de output structure

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  19. Add ciriquant dockerfile

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  20. Update ciriquant docker image

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  21. Change ciriquant de output format to csv

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  22. Fix ciriquant de caching problems

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  23. Fix ciriquant de version capture problems

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  24. Make sure ciriquant de is only executed once per pairing

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  25. Add proper handling of ciriquant RDS

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Commits on Aug 25, 2024

  1. Update ciriquant image

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Commits on Aug 26, 2024

  1. Add retries to some memory intensive processes

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  2. Increase annotation resource label

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  3. Update ciriquant image

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Commits on Aug 27, 2024

  1. Improve ciriquant output directory definition

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  2. Tweak ciriquant publishdir definitions

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  3. Switch miRNA majority vote to polars

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  4. Fix some problems with updated mirna majority vote

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  5. Further improve mirna majority vote performance

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  6. Implement custom sample joining script

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  7. Fix minor bug in new sample joining module

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Commits on Sep 24, 2024

  1. Add default value for mature parameter

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  2. Fix null value in publishDir

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  3. Add quantification_tools to nextflow_schema.json

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Commits on Sep 25, 2024

  1. Fix editorconfig

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  2. Move save_intermediates to less prominent spot in docs

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  3. Simplify parameter docs structure

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  4. Fix schema error

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  5. Move bootstrap samples parameter documentation to more suitable spot

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  6. Change parameter order in nextflow.config

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  7. Remove trailing whitespace

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  8. Add max_shift parameter

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  9. Fix gtftk tabulate bug

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  10. Add custom bed merging

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  11. Fix some custom combine bugs

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Commits on Sep 26, 2024

  1. Unify param names and improve max_shift implementation

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  2. Fix outdir definition

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  3. Merge pull request #172 from nf-core/ciriquant 

    Implement ciriquant quantification
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  4. Merge upset plotting with sample combine_beds

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    nictru committed Sep 26, 2024
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  5. Change the way combine_bed is parametrized

    @nictru
    nictru committed Sep 26, 2024
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  6. Fix empty checks

    @nictru
    nictru committed Sep 26, 2024
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  7. Improve error message on empty

    @nictru
    nictru committed Sep 26, 2024
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  8. Prettier

    @nictru
    nictru committed Sep 26, 2024
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  9. Editorconfig

    @nictru
    nictru committed Sep 26, 2024
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  10. Remove upset process configs

    @nictru
    nictru committed Sep 26, 2024
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  11. Make combine_beds plot outputs optional

    @nictru
    nictru committed Sep 26, 2024
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  12. Merge pull request #173 from nf-core/microshifts 

    Add parameter for grouping detected circRNAs that are very close
    @nictru
    nictru authored Sep 26, 2024
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Commits on Oct 16, 2024

  1. Fix version numbering

    @nictru
    nictru committed Oct 16, 2024
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  2. Add nico as an author

    @nictru
    nictru committed Oct 16, 2024
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  3. Init changelog

    @nictru
    nictru committed Oct 16, 2024
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  4. Fill "added" field in Changelog

    @nictru
    nictru committed Oct 16, 2024
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  5. Fix http json schema URLs

    @nictru
    nictru committed Oct 16, 2024
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  6. Prettier

    @nictru
    nictru committed Oct 16, 2024
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  7. Merge pull request #174 from nf-core/versioning 

    Versioning
    @mashehu
    mashehu authored Oct 16, 2024
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  8. Template update for nf-core/tools version 3.0.2

    @nf-core-bot
    nf-core-bot committed Oct 16, 2024
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  9. Merge branch 'dev' into nf-core-template-merge-3.0.2

    @nictru
    nictru committed Oct 16, 2024
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  10. Remove nf-validation trace

    @nictru
    nictru committed Oct 16, 2024
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  11. Update nextflow required version badge

    @nictru
    nictru committed Oct 16, 2024
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  12. Restructure some param locations to comply with latest schema

    @nictru
    nictru committed Oct 16, 2024
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  13. Update testdata base path references

    @nictru
    nictru committed Oct 16, 2024
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  14. Fix test dataset base path usage

    @nictru
    nictru committed Oct 16, 2024
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  15. Update json schema

    @nictru
    nictru committed Oct 16, 2024
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  16. Fix multiQC call

    @nictru
    nictru committed Oct 16, 2024
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  17. Fix channel structure bug

    Nico Trummer committed Oct 16, 2024
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  18. Remove old way of specifying resource limits

    Nico Trummer committed Oct 16, 2024
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Commits on Oct 18, 2024

  1. Merge pull request #175 from nf-core/nf-core-template-merge-3.0.2 

    Important! Template update for nf-core/tools v3.0.2
    @mweyrich28
    mweyrich28 authored Oct 18, 2024
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