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PR for Release 2.4.0 #446

Merged
merged 414 commits into from
Oct 14, 2024
Merged

PR for Release 2.4.0 #446

merged 414 commits into from
Oct 14, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Sep 4, 2024

  1. Fix #404 

    Fix for #404
    @apeltzer
    apeltzer authored Sep 4, 2024
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  2. Add Fix for 404

    @apeltzer
    apeltzer authored Sep 4, 2024
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  3. Merge pull request #405 from nf-core/fix-404 

    Fix Umicollapse PE wrong method set
    @apeltzer
    apeltzer authored Sep 4, 2024
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  4. add meta to channels

    @atrigila
    atrigila committed Sep 4, 2024
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  5. replace for nf-core modules

    @atrigila
    atrigila committed Sep 4, 2024
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  6. remove unused subworkflow and rename used to main

    @atrigila
    atrigila committed Sep 4, 2024
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  7. emit versions and update test

    @atrigila
    atrigila committed Sep 4, 2024
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  8. Merge pull request #397 from atrigila/nf_core_blat 

    Replace local `blat` for nf-core `blat` in contaminant filter subworkflow
    @apeltzer
    apeltzer authored Sep 4, 2024
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Commits on Sep 5, 2024

  1. remove unused local blat mirna module

    @atrigila
    atrigila committed Sep 5, 2024
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  2. add nf-core mirtrace

    @atrigila
    atrigila committed Sep 5, 2024
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Commits on Sep 6, 2024

  1. update docs

    @atrigila
    atrigila committed Sep 6, 2024
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  2. fastp3 fix

    zxBIB Schcolnicov committed Sep 6, 2024
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  3. Pulled from dev

    zxBIB Schcolnicov committed Sep 6, 2024
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  4. update tests

    @atrigila
    atrigila committed Sep 6, 2024
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  5. Added nftest

    zxBIB Schcolnicov committed Sep 6, 2024
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  6. Merge pull request #412 from nschcolnicov/nextflex 

    Updating nextflex branch
    @nschcolnicov
    nschcolnicov authored Sep 6, 2024
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  7. Update main.nf

    @nschcolnicov
    nschcolnicov authored Sep 6, 2024
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  8. update ci tests nextflex

    @atrigila
    atrigila committed Sep 6, 2024
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Commits on Sep 7, 2024

  1. Merge pull request #386 from nf-core/trim3p_nextflex

    @apeltzer
    apeltzer authored Sep 7, 2024
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  2. Merge pull request #411 from atrigila/mirtrace_migration

    @apeltzer
    apeltzer authored Sep 7, 2024
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Commits on Sep 10, 2024

  1. add nf-core seqcluster

    @atrigila
    atrigila committed Sep 10, 2024
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  2. delete local modules replaced by nf-core

    @atrigila
    atrigila committed Sep 10, 2024
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  3. update tests

    @atrigila
    atrigila committed Sep 10, 2024
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  4. allow config files to be used

    @atrigila
    atrigila committed Sep 10, 2024
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Commits on Sep 11, 2024

  1. update mirtrace/qc

    @atrigila
    atrigila committed Sep 11, 2024
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  2. prepare config if species has mirtrace_species

    @atrigila
    atrigila committed Sep 11, 2024
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  3. update test nextflex

    @atrigila
    atrigila committed Sep 11, 2024
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  4. update changelog

    @atrigila
    atrigila committed Sep 11, 2024
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  5. add transpose

    @atrigila
    atrigila committed Sep 11, 2024
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  6. update snapshots

    @atrigila
    atrigila committed Sep 11, 2024
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  7. update snapshots

    @atrigila
    atrigila committed Sep 11, 2024
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  8. Merge pull request #420 from atrigila/fix_testnextflex 

    Add `config` mode to nf-core `mirtrace/qc`
    @apeltzer
    apeltzer authored Sep 11, 2024
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  9. Merge branch 'dev' into add_nf_core_seqclustre

    @atrigila
    atrigila authored Sep 11, 2024
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  10. update snapshots

    @atrigila
    atrigila committed Sep 11, 2024
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Commits on Sep 12, 2024

  1. Merge pull request #418 from atrigila/add_nf_core_seqclustre 

    Add nf-core `seqcluster` module
    @apeltzer
    apeltzer authored Sep 12, 2024
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  2. correct hsa gff3 path

    @atrigila
    atrigila committed Sep 12, 2024
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  3. add nf-core mirtop

    @atrigila
    atrigila committed Sep 12, 2024
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  4. add nf-core mirtop

    @atrigila
    atrigila committed Sep 12, 2024
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Commits on Sep 13, 2024

  1. Bump versions

    @apeltzer
    apeltzer committed Sep 13, 2024
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  2. Fix litn

    @apeltzer
    apeltzer committed Sep 13, 2024
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  3. Fix version to 23.10

    @apeltzer
    apeltzer committed Sep 13, 2024
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  4. Merge pull request #425 from nf-core/bump-minimum-nxf-version

    @apeltzer
    apeltzer authored Sep 13, 2024
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  5. update mirtop with arity

    @atrigila
    atrigila committed Sep 13, 2024
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  6. use all bams

    @atrigila
    atrigila committed Sep 13, 2024
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  7. add config for mirtop

    @atrigila
    atrigila committed Sep 13, 2024
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  8. use all bams

    @atrigila
    atrigila committed Sep 13, 2024
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  9. add new search pattern for mirtop

    @atrigila
    atrigila committed Sep 13, 2024
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  10. update tests

    @atrigila
    atrigila committed Sep 13, 2024
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  11. Merge remote-tracking branch 'origin/dev' into add_nf_core_mirtop

    @atrigila
    atrigila committed Sep 13, 2024
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  12. update tests

    @atrigila
    atrigila committed Sep 13, 2024
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Commits on Sep 16, 2024

  1. emit a warning upon suply of PE data

    @atrigila
    atrigila committed Sep 16, 2024
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  2. add nf-core pigz uncompress

    @atrigila
    atrigila committed Sep 16, 2024
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  3. update changelog

    @atrigila
    atrigila committed Sep 16, 2024
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  4. update changelog

    @atrigila
    atrigila committed Sep 16, 2024
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  5. Merge pull request #426 from atrigila/add_nf_core_mirtop 

    Add nf-core `mirtop`
    @apeltzer
    apeltzer authored Sep 16, 2024
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  6. allow to save intermediates

    @atrigila
    atrigila committed Sep 16, 2024
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  7. copy staged files

    @atrigila
    atrigila committed Sep 16, 2024
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  8. remove unused local module

    @atrigila
    atrigila committed Sep 16, 2024
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  9. Merge branch 'dev' into add_pigz

    @atrigila
    atrigila authored Sep 16, 2024
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  10. remove unused local mirtop

    @atrigila
    atrigila committed Sep 16, 2024
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  11. remove unused local mirtop quant

    @atrigila
    atrigila committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. Merge branch 'dev' into save_intermediates

    @atrigila
    atrigila authored Sep 17, 2024
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  2. Merge branch 'dev' into pe_warning

    @atrigila
    atrigila authored Sep 17, 2024
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  3. prettify

    @atrigila
    atrigila committed Sep 17, 2024
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  4. prettify

    @atrigila
    atrigila committed Sep 17, 2024
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  5. default to false

    @atrigila
    atrigila committed Sep 17, 2024
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  6. fix linting

    @atrigila
    atrigila committed Sep 17, 2024
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  7. Merge pull request #429 from atrigila/save_intermediates 

    allow to save intermediates
    @atrigila
    atrigila authored Sep 17, 2024
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  8. Merge branch 'dev' into pe_warning

    @atrigila
    atrigila authored Sep 17, 2024
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  9. Merge branch 'dev' into add_pigz

    @apeltzer
    apeltzer authored Sep 17, 2024
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  10. save intermediates in tests

    @atrigila
    atrigila committed Sep 17, 2024
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  11. Merge branch 'add_pigz' of https://github.com/atrigila/smrnaseq into … 

    …add_pigz
    @atrigila
    atrigila committed Sep 17, 2024
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  12. save intermediates

    @atrigila
    atrigila committed Sep 17, 2024
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  13. Merge pull request #427 from atrigila/add_pigz 

    Add nf-core `pigz uncompress`
    @atrigila
    atrigila authored Sep 17, 2024
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  14. Merge branch 'dev' into pe_warning

    @atrigila
    atrigila authored Sep 17, 2024
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Commits on Sep 18, 2024

  1. Merge pull request #430 from atrigila/pe_warning 

    Emit a warning upon supply of PE data
    @apeltzer
    apeltzer authored Sep 18, 2024
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  2. update multiqc

    @atrigila
    atrigila committed Sep 18, 2024
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  3. Merge remote-tracking branch 'origin/dev' into upgrade_multiqc

    @atrigila
    atrigila committed Sep 18, 2024
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  4. update file names

    @atrigila
    atrigila committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. update tests

    @atrigila
    atrigila committed Sep 19, 2024
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  2. update tests

    @atrigila
    atrigila committed Sep 19, 2024
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  3. update changelog

    @atrigila
    atrigila committed Sep 19, 2024
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  4. update modules

    @atrigila
    atrigila committed Sep 19, 2024
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  5. cpus ci github

    @atrigila
    atrigila committed Sep 19, 2024
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  6. replace local modules for nf-core bowtie

    @atrigila
    atrigila committed Sep 19, 2024
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  7. change to value channels

    @atrigila
    atrigila committed Sep 19, 2024
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  8. update tests

    @atrigila
    atrigila committed Sep 19, 2024
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  9. update changelog

    @atrigila
    atrigila committed Sep 19, 2024
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  10. Merge pull request #432 from atrigila/upgrade_multiqc

    @apeltzer
    apeltzer authored Sep 19, 2024
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  11. Merge branch 'dev' into migrate_nf-core_bowtie

    @atrigila
    atrigila authored Sep 19, 2024
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Commits on Sep 20, 2024

  1. update tests

    @atrigila
    atrigila committed Sep 20, 2024
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  2. Merge pull request #435 from atrigila/migrate_nf-core_bowtie 

    Migrate to nf-core `bowtie build`
    @apeltzer
    apeltzer authored Sep 20, 2024
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  3. parallelize mirtop and join results

    @atrigila
    atrigila committed Sep 20, 2024
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  4. Merge remote-tracking branch 'origin/dev' into update_mirtop

    @atrigila
    atrigila committed Sep 20, 2024
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  5. update tests

    @atrigila
    atrigila committed Sep 20, 2024
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  6. update changelog

    @atrigila
    atrigila committed Sep 20, 2024
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  7. update tests

    @atrigila
    atrigila committed Sep 20, 2024
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  8. Merge pull request #438 from atrigila/update_mirtop

    @apeltzer
    apeltzer authored Sep 20, 2024
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Commits on Sep 23, 2024

  1. import bowtie2 align

    @atrigila
    atrigila committed Sep 23, 2024
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  2. remove dumps

    @atrigila
    atrigila committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. add meta

    @atrigila
    atrigila committed Sep 24, 2024
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  2. add tag and use a single stats file

    @atrigila
    atrigila committed Sep 24, 2024
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  3. add config for new modules

    @atrigila
    atrigila committed Sep 24, 2024
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  4. migrate trna and cdna

    @atrigila
    atrigila committed Sep 24, 2024
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  5. add meta contaminant to reads and process

    @atrigila
    atrigila committed Sep 24, 2024
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  6. add config to bowtie align

    @atrigila
    atrigila committed Sep 24, 2024
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  7. Fix paired end sample handling

    zxBIB Schcolnicov committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. optionally emit fastq

    @atrigila
    atrigila committed Sep 25, 2024
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  2. add metamap

    @atrigila
    atrigila committed Sep 25, 2024
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  3. migrate contamination filter to nf-core modules

    @atrigila
    atrigila committed Sep 25, 2024
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  4. add config for contamination

    @atrigila
    atrigila committed Sep 25, 2024
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  5. remove unused local module

    @atrigila
    atrigila committed Sep 25, 2024
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  6. remove dumps

    @atrigila
    atrigila committed Sep 25, 2024
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  7. Merge remote-tracking branch 'origin/dev' into nf-core_bowtie_align

    @atrigila
    atrigila committed Sep 25, 2024
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  8. update tests

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  9. update tests and changelog

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  10. Merge pull request #439 from nschcolnicov/issue_415 

    Fix paired end sample handling
    @nschcolnicov
    nschcolnicov authored Sep 25, 2024
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  11. Merge remote-tracking branch 'origin/dev' into nf-core_bowtie_align

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  12. update changelog

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  13. Added info about read number behavior

    zxBIB Schcolnicov committed Sep 25, 2024
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  14. Remove trailing space

    zxBIB Schcolnicov committed Sep 25, 2024
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  15. Ran precommit

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  16. Updated mirna_quant

    zxBIB Schcolnicov committed Sep 25, 2024
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  17. Updated genome_quant and config

    zxBIB Schcolnicov committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. Merge pull request #441 from atrigila/nf-core_bowtie_align 

    Migrate to nf-core `bowtie align` in contaminant filter
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  2. Merge pull request #442 from nschcolnicov/issue_94 

    Added info about read number behavior
    @apeltzer
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  3. Update README.md

    @apeltzer
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  4. Updated snap tool versions

    zxBIB Schcolnicov committed Sep 26, 2024
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  5. Merge branch 'dev' of https://github.com/nf-core/smrnaseq into migrat… 

    …e_bowtie
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  6. Merge pull request #444 from nschcolnicov/migrate_bowtie 

    Migrate bowtie
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  7. Merge pull request #445 from nf-core/add-credits 

    Add some more credits
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  8. General cleanup

    zxBIB Schcolnicov committed Sep 26, 2024
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  9. Pre-commit

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  10. CHanges in mirdeep and updated bowtie_index channel description

    zxBIB Schcolnicov committed Sep 26, 2024
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  11. erge branch 'issue_400' of https://github.com/nschcolnicov/smrnaseq i… 

    …nto issue_400

 Please enter a commit message to explain why this merge is necessary,
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  12. add nf-core mirdeep

    @atrigila
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  13. add nf-core mirdeep2

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  14. update tests

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  15. add mirdeep test

    @atrigila
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  16. update config

    @atrigila
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  17. update docs

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  18. make has fasta/index explicit for mirdeep

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  19. Revert "make has fasta/index explicit for mirdeep" 

    This reverts commit 04b65eb.
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  20. update changelog

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  21. remove local unused modules

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  22. Revert "remove local unused modules" 

    This reverts commit f40a757.
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Commits on Sep 27, 2024

  1. remove local mirdeep

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  2. Merge pull request #448 from atrigila/add_mirdeep_sbwf 

    Add nf-core `mirdeep2` and a test case
    @atrigila
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  3. Pulled from dev

    zxBIB Schcolnicov committed Sep 27, 2024
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  4. renamed missing variables

    zxBIB Schcolnicov committed Sep 27, 2024
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Commits on Sep 30, 2024

  1. Addressing PR comments

    @nschcolnicov
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  2. Updated datatable module nftest

    @nschcolnicov
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  3. Addressing PR comments

    zxBIB Schcolnicov committed Sep 30, 2024
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  4. Merge pull request #447 from nschcolnicov/issue_400

    @apeltzer
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  5. Removed untar, updated bowtie_channel

    zxBIB Schcolnicov committed Sep 30, 2024
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  6. update tests

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Commits on Oct 1, 2024

  1. Update untar module config

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  2. Update changelog

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    nschcolnicov committed Oct 1, 2024
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  3. Merge pull request #452 from nschcolnicov/standardize_bowtie 

    Removed untar, updated bowtie_channel
    @nschcolnicov
    nschcolnicov authored Oct 1, 2024
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  4. Merge pull request #454 from atrigila/fix_test_edger 

    Fix test edgeR
    @atrigila
    atrigila authored Oct 1, 2024
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  5. Removed unused protocol argument and updated docs

    zxBIB Schcolnicov committed Oct 1, 2024
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  6. move clean fasta

    @atrigila
    atrigila committed Oct 1, 2024
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  7. update tests and changelog

    @atrigila
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Commits on Oct 2, 2024

  1. Merge pull request #457 from atrigila/move_clean_fasta 

    Reorganize `clean fasta` code
    @atrigila
    atrigila authored Oct 2, 2024
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  2. update modules

    @atrigila
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  3. collect missing version

    @atrigila
    atrigila committed Oct 2, 2024
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  4. update subworkflows

    @atrigila
    atrigila committed Oct 2, 2024
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  5. update reference text

    @atrigila
    atrigila committed Oct 2, 2024
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  6. add tool citations

    @atrigila
    atrigila committed Oct 2, 2024
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  7. update tests

    @atrigila
    atrigila committed Oct 2, 2024
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  8. update changelog

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  9. Merge pull request #459 from atrigila/fix_linting 

    Update modules and subworkflows, fix linting
    @atrigila
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  10. Merge pull request #456 from nschcolnicov/issue_366 

    Removed unused protocol argument and updated docs
    @nschcolnicov
    nschcolnicov authored Oct 2, 2024
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Commits on Oct 3, 2024

  1. Update usage.md

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    nschcolnicov committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. Updated docs

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  2. fix: wrapping 0 in fasta files

    @atrigila
    atrigila committed Oct 4, 2024
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  3. do not publish intermediate files

    @atrigila
    atrigila committed Oct 4, 2024
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  4. minor grammar and typo fixes

    @atrigila
    atrigila committed Oct 4, 2024
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  5. update changelog

    @atrigila
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  6. Merge pull request #462 from atrigila/test_release 

    Fix wrapping in fasta files
    @nschcolnicov
    nschcolnicov authored Oct 4, 2024
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  7. Pulled from dev

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  8. Updated docs

    @nschcolnicov
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  9. Apply suggestions from code review 

    Co-authored-by: Anabella Trigila <[email protected]>
    @nschcolnicov @atrigila
    nschcolnicov and atrigila authored Oct 4, 2024
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  10. Addressed PR comments

    @nschcolnicov
    nschcolnicov committed Oct 4, 2024
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  11. Fixed formating

    @nschcolnicov
    nschcolnicov committed Oct 4, 2024
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  12. Fix render formating

    @nschcolnicov
    nschcolnicov committed Oct 4, 2024
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  13. Merge pull request #461 from nf-core/update_docs 

    Update usage.md
    @nschcolnicov
    nschcolnicov authored Oct 4, 2024
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  14. Add multiqc 1.25.1 and update changelog with software

    @apeltzer
    apeltzer committed Oct 4, 2024
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  15. Add more software updates

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Commits on Oct 5, 2024

  1. Merge pull request #463 from nf-core/update-software-modules

    @apeltzer
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Commits on Oct 6, 2024

  1. Add licences and authorship information

    @apeltzer
    apeltzer committed Oct 6, 2024
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  2. Improve changelog

    @apeltzer
    apeltzer committed Oct 6, 2024
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  3. Date + Bump version

    @apeltzer
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  4. Merge pull request #464 from nf-core/licences 

    Add licences and authorship information
    @apeltzer
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  5. Merge pull request #466 from nf-core/bump-release 

    Date + Bump version
    @apeltzer
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Commits on Oct 7, 2024

  1. PULL_REQUEST_TEMPLATE.md aktualisieren 

    Co-authored-by: Anabella Trigila <[email protected]>
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    apeltzer and atrigila authored Oct 7, 2024
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  2. CHANGELOG.md aktualisieren 

    Co-authored-by: Anabella Trigila <[email protected]>
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    apeltzer and atrigila authored Oct 7, 2024
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  3. usage.md aktualisieren 

    Co-authored-by: Anabella Trigila <[email protected]>
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    apeltzer and atrigila authored Oct 7, 2024
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  4. output.md aktualisieren 

    Co-authored-by: Anabella Trigila <[email protected]>
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Commits on Oct 8, 2024

  1. Update subworkflows/local/prepare_genome/main.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @apeltzer @jfy133
    apeltzer and jfy133 authored Oct 8, 2024
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  2. Couple of minor issues resolved from reviews

    @apeltzer
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  3. Add hint to license

    @apeltzer
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  4. Put in links

    @apeltzer
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  5. Update nextflow_schema.json 

    Co-authored-by: James A. Fellows Yates <[email protected]>
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  6. Update subworkflows/local/contaminant_filter/main.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
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    apeltzer and jfy133 authored Oct 8, 2024
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  7. Update subworkflows/local/mirna_quant.nf 

    Co-authored-by: James A. Fellows Yates <[email protected]>
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    apeltzer and jfy133 authored Oct 8, 2024
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  8. Bump release date

    @apeltzer
    apeltzer committed Oct 8, 2024
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  9. Fix tests

    @apeltzer
    apeltzer committed Oct 8, 2024
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  10. address Change to = assignment, see above #470

    @atrigila
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  11. Fix tests for release PR

    @apeltzer
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  12. Merge branch 'adress-issues' of https://github.com/nf-core/smrnaseq i… 

    …nto adress-issues
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  13. Address Make citation tools dependent on whether tool was executed #468

    @atrigila
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  14. Template update for nf-core/tools version 3.0.0

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  15. Pulled from dev

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  16. Merge branch 'dev' into adress-issues

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  17. Pulled from dev

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  18. Revert changes in ci.yml

    @nschcolnicov
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  19. Test ci config profile

    @nschcolnicov
    nschcolnicov committed Oct 8, 2024
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  20. Update ci config profile

    @nschcolnicov
    nschcolnicov committed Oct 8, 2024
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  21. Update snaps

    @nschcolnicov
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Commits on Oct 9, 2024

  1. Template update for nf-core/tools version 3.0.1

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  2. Pulled from template 3.0.1

    @nschcolnicov
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Commits on Oct 10, 2024

  1. validate input params

    @atrigila
    atrigila committed Oct 10, 2024
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  2. add igenomes base

    @atrigila
    atrigila committed Oct 10, 2024
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  3. Remove level 1 hearder mark in list.

    @charles-plessy
    charles-plessy authored Oct 10, 2024
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Commits on Oct 11, 2024

  1. template_version_comment.yml aktualisieren 

    Co-authored-by: Louis LE NEZET <[email protected]>
    @apeltzer @LouisLeNezet
    apeltzer and LouisLeNezet authored Oct 11, 2024
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  2. Remove todo

    @apeltzer
    apeltzer committed Oct 11, 2024
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  3. Merge pull request #472 from nf-core/nf-core/tools/3.0.0 

    Template update 3.0.1
    @apeltzer
    apeltzer authored Oct 11, 2024
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  4. Merge remote-tracking branch 'origin/dev' into adress-issues

    @apeltzer
    apeltzer committed Oct 11, 2024
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  5. Final update of modules and subworkflows

    @apeltzer
    apeltzer committed Oct 11, 2024
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  6. Remove one more todo

    @apeltzer
    apeltzer committed Oct 11, 2024
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  7. Template update for nf-core/tools version 3.0.2

    @nf-core-bot
    nf-core-bot committed Oct 11, 2024
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  8. Merged the template

    @apeltzer
    apeltzer committed Oct 11, 2024
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  9. Also remove .nf-test directory

    @apeltzer
    apeltzer committed Oct 11, 2024
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  10. Fix merge issue

    @apeltzer
    apeltzer committed Oct 11, 2024
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  11. Fixing duplicate imports

    @apeltzer
    apeltzer committed Oct 11, 2024
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  12. Hopefully fix

    @apeltzer
    apeltzer committed Oct 11, 2024
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  13. Finding more issues

    @apeltzer
    apeltzer committed Oct 11, 2024
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  14. Date++

    @apeltzer
    apeltzer committed Oct 11, 2024
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Commits on Oct 13, 2024

  1. Remove some lines

    @apeltzer
    apeltzer committed Oct 13, 2024
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  2. Update modules

    @apeltzer
    apeltzer committed Oct 13, 2024
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  3. remove duplicates from new template

    @atrigila
    atrigila committed Oct 13, 2024
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  4. remove extra argument, add missing {

    @atrigila
    atrigila committed Oct 13, 2024
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  5. correct schema structure

    @atrigila
    atrigila committed Oct 13, 2024
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  6. fix linting errors

    @atrigila
    atrigila committed Oct 13, 2024
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Commits on Oct 14, 2024

  1. Merge pull request #469 from nf-core/adress-issues 

    Adress issues from review
    @apeltzer
    apeltzer authored Oct 14, 2024
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  2. Tiny bugfixes

    @apeltzer
    apeltzer committed Oct 14, 2024
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  3. Update CITATIONS.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
    @apeltzer @mashehu
    apeltzer and mashehu authored Oct 14, 2024
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  4. Merge pull request #476 from nf-core/tiny-fixes 

    Tiny bugfixes
    @apeltzer
    apeltzer authored Oct 14, 2024
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  5. Fix tiny issue with linting

    @apeltzer
    apeltzer committed Oct 14, 2024
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