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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 Feb 1, 2024

  1. pull logo changes manually from TEMPLATE

    @mashehu
    mashehu committed Feb 1, 2024
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  2. Merge branch 'nf-core-template-merge-2.12' of https://github.com/Mari… 

    …ekeVromman/circrna into nf-core-template-merge-2.12
    @mashehu
    mashehu committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. fix typo in docs/output.md 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @MariekeVromman @mashehu
    MariekeVromman and mashehu committed Feb 2, 2024
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  2. remove redundant output declaration

    @MariekeVromman
    MariekeVromman committed Feb 2, 2024
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  3. Merge pull request #96 from MariekeVromman/nf-core-template-merge-2.12 

    Nf core template merge 2.12
    @MariekeVromman
    MariekeVromman committed Feb 2, 2024
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Commits on Feb 14, 2024

  1. make /tmp dir in work dir (sort) to avoid error on cluster

    @MariekeVromman
    MariekeVromman committed Feb 14, 2024
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  2. add tmp dir

    @MariekeVromman
    MariekeVromman committed Feb 14, 2024
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  3. Update modules/local/star/sjdb/main.nf 

    Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
    @MariekeVromman @mashehu
    MariekeVromman and mashehu committed Feb 14, 2024
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  4. fix indentation

    @MariekeVromman
    MariekeVromman committed Feb 14, 2024
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  5. clean up fasta (not working correctly yet)

    @MariekeVromman
    MariekeVromman committed Feb 14, 2024
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Commits on Feb 19, 2024

  1. fix value channel for star index

    @MariekeVromman
    MariekeVromman committed Feb 19, 2024
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  2. Merge pull request #98 from MariekeVromman/dev 

    resolve error for tmp dir when running 'sort' on cluster
resolve only one sample running when using star parameter (was a queue channel instead of value channel)
    @MariekeVromman
    MariekeVromman committed Feb 19, 2024
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Commits on Feb 20, 2024

  1. resolve gawk bug, prefix/sufix issue and publish dir

    @MariekeVromman
    MariekeVromman committed Feb 20, 2024
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  2. Template update for nf-core/tools version 2.13

    @nf-core-bot
    nf-core-bot committed Feb 20, 2024
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Commits on Feb 22, 2024

  1. try to fix disapearing folder

    @MariekeVromman
    MariekeVromman committed Feb 22, 2024
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  2. try to fix naming

    @MariekeVromman
    MariekeVromman committed Feb 22, 2024
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  3. try to fix basename

    @MariekeVromman
    MariekeVromman committed Feb 22, 2024
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  4. change order

    @MariekeVromman
    MariekeVromman committed Feb 22, 2024
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  5. update naming new fasta file

    @MariekeVromman
    MariekeVromman committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. update gawk module

    @MariekeVromman
    MariekeVromman committed Feb 23, 2024
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Commits on Feb 28, 2024

  1. Template update for nf-core/tools version 2.13

    @nf-core-bot @nictru
    nf-core-bot authored and nictru committed Feb 28, 2024
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  2. Merge branch 'nf-core-template-merge-2.13' of github.com:nf-core/circ… 

    …rna into nf-core-template-merge-2.13
    @nictru
    nictru committed Feb 28, 2024
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Commits on Feb 29, 2024

  1. Implement pipeline changes necessary for the 2.13 tools update

    @nictru
    nictru committed Feb 29, 2024
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  2. Fix some more problems with template update

    @nictru
    nictru committed Feb 29, 2024
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  3. Fix linting problems

    @nictru
    nictru committed Feb 29, 2024
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  4. Template update for nf-core/tools version 2.13.1

    @nf-core-bot
    nf-core-bot committed Feb 29, 2024
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  5. Merge branch 'nf-core-template-merge-2.13' into nf-core-template-merg… 

    …e-2.13.1
    @nictru
    nictru committed Feb 29, 2024
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  6. Merge pull request #101 from nf-core/nf-core-template-merge-2.13.1 

    Important! Template update for nf-core/tools v2.13.1
    @nictru
    nictru committed Feb 29, 2024
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Commits on Mar 1, 2024

  1. Implement pandas-based annotation

    @nictru
    nictru committed Mar 1, 2024
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  2. Implement handling of intergenic circRNAs

    @nictru
    nictru committed Mar 1, 2024
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  3. Fix linting problems

    @nictru
    nictru committed Mar 1, 2024
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  4. Implement handling of "gene" rows in annotation

    @nictru
    nictru committed Mar 1, 2024
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  5. Remove quay.io prefix from container definition 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
    @nictru @maxulysse
    nictru and maxulysse committed Mar 1, 2024
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  6. Implement capture of versions in annotation

    @nictru
    nictru committed Mar 1, 2024
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  7. Fix linting

    @nictru
    nictru committed Mar 1, 2024
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  8. Fix problem with annotation.py script calling

    @nictru
    nictru committed Mar 1, 2024
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  9. Fix problem with escape characters in dedicated python script

    @nictru
    nictru committed Mar 1, 2024
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  10. Merge branch 'dev' into clean_fasta

    @MariekeVromman
    MariekeVromman committed Mar 1, 2024
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  11. Merge pull request #95 from nf-core/parallel-annotation 

    Impove annotation performance
    @nictru
    nictru committed Mar 1, 2024
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  12. merge with dev to get new tool version

    @MariekeVromman
    MariekeVromman committed Mar 1, 2024
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  13. add dumpsoftwareversions

    @MariekeVromman
    MariekeVromman committed Mar 1, 2024
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Commits on Mar 3, 2024

  1. Fix script references

    @nictru
    nictru committed Mar 3, 2024
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Commits on Mar 7, 2024

  1. Merge pull request #103 from nf-core/102-problems-with-scripts-refere… 

    …nced-using-the-$workflowprojectdir-variable

Fix script references
    @nictru
    nictru committed Mar 7, 2024
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Commits on Mar 12, 2024

  1. Merge pull request #100 from MariekeVromman/clean_fasta 

    Clean fasta file (required for mapsplice)
    @MariekeVromman
    MariekeVromman committed Mar 12, 2024
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Commits on Mar 18, 2024

  1. Improve channel structure

    @nictru
    nictru committed Mar 18, 2024
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  2. Implement seqkit_split

    @nictru
    nictru committed Mar 18, 2024
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  3. Update seqkit version

    @nictru
    nictru committed Mar 18, 2024
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  4. Update modules

    @nictru
    nictru committed Mar 18, 2024
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  5. Fix some common problems in CIRIquant and HISAT2_ALIGN

    @nictru
    nictru committed Mar 18, 2024
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  6. Fix miranda channel structure

    @nictru
    nictru committed Mar 18, 2024
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  7. Fix linting

    @nictru
    nictru committed Mar 18, 2024
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  8. Add some meta inputs

    @nictru
    nictru committed Mar 18, 2024
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  9. Prettier

    @nictru
    nictru committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. Unify species_id parameter

    @nictru
    nictru committed Mar 19, 2024
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  2. Simplify handling of tool indices

    @nictru
    nictru committed Mar 19, 2024
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  3. Add defaults for previously undefined parameters

    @nictru
    nictru committed Mar 19, 2024
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  4. Linting

    @nictru
    nictru committed Mar 19, 2024
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  5. Fix indent

    @nictru
    nictru committed Mar 19, 2024
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Commits on Mar 21, 2024

  1. Merge pull request #104 from nf-core/improve-genome-preparation 

    Fix some general pipeline problems
    @nictru
    nictru committed Mar 21, 2024
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Commits on Mar 30, 2024

  1. Make some parameters non-required when according modules are disabled

    @nictru
    nictru committed Mar 30, 2024
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Commits on Apr 2, 2024

  1. Merge pull request #107 from nf-core/fix-falsely-required-parameters 

    Fix falsely required parameters
    @nictru
    nictru committed Apr 2, 2024
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Commits on Apr 11, 2024

  1. fix hisast2 index bug in yml file

    @MariekeVromman
    MariekeVromman committed Apr 11, 2024
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  2. fix bug to make dir

    @MariekeVromman
    MariekeVromman committed Apr 11, 2024
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  3. cleaner way to set hisat2_prefix

    @MariekeVromman
    MariekeVromman committed Apr 11, 2024
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  4. revert back changes for testing

    @MariekeVromman
    MariekeVromman committed Apr 11, 2024
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Commits on Apr 15, 2024

  1. Merge pull request #109 from MariekeVromman/ciriquant_bug 

    Resolving tiny ciriquant bug
    @nictru
    nictru committed Apr 15, 2024
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  2. Add parameter for setting STAR limitSjdbInsertNsj

    @nictru
    nictru committed Apr 15, 2024
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Commits on Apr 16, 2024

  1. Merge pull request #110 from nf-core/star-sjdb-limit 

    Add parameter for setting STAR limitSjdbInsertNsj
    @nictru
    nictru committed Apr 16, 2024
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Commits on Apr 19, 2024

  1. Remove problematic ciriquant-yml process

    @nictru
    nictru committed Apr 19, 2024
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Commits on Apr 20, 2024

  1. Merge pull request #113 from nf-core/ciriquant-yml 

    Remove problematic ciriquant-yml process
    @nictru
    nictru committed Apr 20, 2024
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  2. Implement common quantification

    @nictru
    nictru committed Apr 20, 2024
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  3. Add marking of circRNAs in quantification

    @nictru
    nictru committed Apr 20, 2024
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  4. Increase resources for PSIRC

    @nictru
    nictru committed Apr 20, 2024
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  5. Implement separation of circular and linear counts

    @nictru
    nictru committed Apr 20, 2024
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  6. Implement aggregation of annotations

    @nictru
    nictru committed Apr 20, 2024
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  7. Update quantification subworkflow

    @nictru
    nictru committed Apr 20, 2024
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  8. Simplify count merging processes

    @nictru
    nictru committed Apr 20, 2024
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  9. Use tximport

    @nictru
    nictru committed Apr 20, 2024
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  10. Finalize quantification

    @nictru
    nictru committed Apr 20, 2024
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  11. Implement quantification aggregation for TPMs

    @nictru
    nictru committed Apr 20, 2024
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  12. Override publishdir of quantification results

    @nictru
    nictru committed Apr 20, 2024
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  13. Emit Quantification results

    @nictru
    nictru committed Apr 20, 2024
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  14. Align indentation

    @nictru
    nictru committed Apr 20, 2024
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  15. Remove traces of old count combination

    @nictru
    nictru committed Apr 20, 2024
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  16. Fix compatibility issues with DGEA

    @nictru
    nictru committed Apr 20, 2024
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  17. Add version captures

    @nictru
    nictru committed Apr 20, 2024
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  18. Fix unchanged file

    @nictru
    nictru committed Apr 20, 2024
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  19. Update modules

    @nictru
    nictru committed Apr 20, 2024
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  20. Add missing version capture for ciriquant_yml

    @nictru
    nictru committed Apr 20, 2024
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  21. Fix some version capture problems

    @nictru
    nictru committed Apr 20, 2024
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  22. Fix missing version variable in psirc-quant

    @nictru
    nictru committed Apr 20, 2024
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  23. Revert "Fix unchanged file" 

    This reverts commit 18673fc.
    @nictru
    nictru committed Apr 20, 2024
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  24. Fix editorconfig checks

    @nictru
    nictru committed Apr 20, 2024
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  25. Use gene names for annotation instead of ids

    @nictru
    nictru committed Apr 20, 2024
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  26. Add GTF creation to annotation

    @nictru
    nictru committed Apr 20, 2024
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  27. Switch to processing circRNAs more like standard transcripts

    @nictru
    nictru committed Apr 20, 2024
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  28. Switch to using CSVTK for joining quantifications

    @nictru
    nictru committed Apr 20, 2024
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  29. Implement splitting of circular and linear transcripts

    @nictru
    nictru committed Apr 20, 2024
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  30. Simplify quantification script

    @nictru
    nictru committed Apr 20, 2024
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  31. Add quantification type splitting to output

    @nictru
    nictru committed Apr 20, 2024
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  32. Add filter for overlong circRNAs

    @nictru
    nictru committed Apr 20, 2024
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  33. Remove ciriquant YML version capture

    @nictru
    nictru committed Apr 20, 2024
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  34. Add draft tximeta support

    @nictru
    nictru committed Apr 20, 2024
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  35. Fix problem with erroneous abundance.h5 detection

    @nictru
    nictru committed Apr 20, 2024
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  36. Update tximeta script

    @nictru
    nictru committed Apr 20, 2024
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  37. Switch to tximeta pure RDS approach

    @nictru
    nictru committed Apr 20, 2024
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  38. Implement basic swish functionality

    @nictru
    nictru committed Apr 20, 2024
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  39. Fix linting

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  40. Prettier

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Commits on Apr 21, 2024

  1. Increase resource usage of quantification joining

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  2. Implement separate process for merging summarizedexperiment objects

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Commits on Apr 24, 2024

  1. Fix problematic stub in FISHPOND_SWISH

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  2. Add bam file output to psirc-quant

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  3. Remove swish traces

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  4. Remove check for overlong circRNAs

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Commits on Apr 25, 2024

  1. Fix environment int COUNTS_COMBINED

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  2. Remove quay.io prefixes

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  3. Fix environment definition of MERGE_TOOLS

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  4. Merge pull request #106 from nf-core/common-quantification 

    Implement common quantification
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Commits on May 8, 2024

  1. Template update for nf-core/tools version 2.14.0

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Commits on May 9, 2024

  1. Merge remote-tracking branch 'origin/dev' into nf-core-template-merge… 

    …-2.14.0
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  2. Template update for nf-core/tools version 2.14.1

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  3. Merge branch 'nf-core-template-merge-2.14.0' into nf-core-template-me… 

    …rge-2.14.1
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  4. Remove unnecessary module configs

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  5. Update modules

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  6. Add samtools faidx version capture

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  7. Remove unnecessary nextflow schema entry

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Commits on May 10, 2024

  1. Merge pull request #120 from nf-core/nf-core-template-merge-2.14.1 

    Important! Template update for nf-core/tools v2.14.1
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  2. Implement process for removing overlong transcripts

    @nictru
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  3. Use only merged circRNAs in further analyses

    @nictru
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  4. Implement upset plots

    @nictru
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  5. Refine upset functionality

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  6. Add upset plots to multiqc

    @nictru
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  7. Fix linting

    @nictru
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  8. Fix pandas bug

    @nictru
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  9. Disable upset plots if only one tool is enabled

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  10. Add annotation as rowdata to summarizedExperiment

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  11. Prepare for TPM addition

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  12. Fix DeSeq compatibility problems

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  13. Add TPM the quantification RDS

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  14. Merge pull request #117 from nf-core/exclude-overlong-transcripts 

    Fix some bugs and add upset plots
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Commits on May 22, 2024

  1. Fix GTF attribute splitting

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    nictru committed May 22, 2024
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  2. Simplify FASTA extraction

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    nictru committed May 22, 2024
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  3. Merge pull request #121 from nf-core/mysolid-bugs 

    Fix bugs pointed out by @mysolid on slack
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Commits on May 24, 2024

  1. Simplify STAR and SEGEMEHL discovery

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  2. Simplify CIRCEXPLORER2 workflow

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  3. Simplify CIRCRNA_FINDER

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  4. Simplify FIND_CIRC

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    nictru committed May 24, 2024
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  5. Simplify CIRIQUANT

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    nictru committed May 24, 2024
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  6. Simplify DCC

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  7. Simplify MAPSPLICE

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    nictru committed May 24, 2024
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  8. Restructure discovery tool calls

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  9. Restructure discovery downstream workflows

    @nictru
    nictru committed May 24, 2024
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  10. Simplify annotation workflow

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    nictru committed May 24, 2024
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  11. Change the way discovery tools are disabled

    @nictru
    nictru committed May 24, 2024
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  12. Switch segemehl to bed output

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    nictru committed May 24, 2024
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  13. Implement central BSJ filtering

    @nictru
    nictru committed May 24, 2024
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  14. Implement circexplorer2 unification

    @nictru
    nictru committed May 24, 2024
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  15. Unify find_circ

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    nictru committed May 24, 2024
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  16. Unify ciriquant

    @nictru
    nictru committed May 24, 2024
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  17. Unify DCC

    @nictru
    nictru committed May 24, 2024
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  18. Unify mapsplice

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    nictru committed May 24, 2024
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  19. Unify circrna_finder

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    nictru committed May 24, 2024
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  20. Rename RUN to MAIN in all occurrences

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  21. Add circrna_finder unify version capture

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  22. Remove tool-specific filtering artifacts

    @nictru
    nictru committed May 24, 2024
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  23. Remove technical debt with former "results" channel

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  24. Remove unnecessary checks if circrna_discovery is enabled

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Commits on May 27, 2024

  1. Fix code style problems

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    nictru committed May 27, 2024
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Commits on May 28, 2024

  1. Merge pull request #122 from nf-core/discovery-splitup 

    Simplify circrna_discovery subworkflow
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    nictru committed May 28, 2024
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Commits on May 30, 2024

  1. Update nf-core modules

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    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

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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

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

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  9. Add strandedness to bowtie2 calls

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

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

  1. Add strandedness documentation

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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

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    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
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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

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  10. Switch to template syntax in merge_tools

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  11. Remove custom DESeq2 module

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    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

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Commits on Jun 12, 2024

  1. Remove traces of differential_expression in docs

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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>
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    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

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    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

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

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    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
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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

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    nictru committed Jun 14, 2024
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  16. Prettier

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    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
    @nictru
    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
    @nictru
    nictru committed Jun 19, 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

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    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
    @nictru
    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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