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v2.2.0 release #203

Merged
merged 130 commits into from
Mar 20, 2023
Merged

v2.2.0 release #203

merged 130 commits into from
Mar 20, 2023

Commits on Oct 6, 2022

  1. Bump to 2.1.1dev

    @apeltzer
    apeltzer committed Oct 6, 2022
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  2. Merge pull request #155 from nf-core/bump-dev 

    Bump to 2.1.1dev
    @apeltzer
    apeltzer committed Oct 6, 2022
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Commits on Oct 11, 2022

  1. Removed function get_samplesheet_paths which is replicated in subwork… 

    …flows/local/input_check.nf
    Alison Meynert committed Oct 11, 2022
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  2. Samplesheet documentation includes expected cells and sequencing center

    Alison Meynert committed Oct 11, 2022
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  3. Validation of optional samplesheet columns expected_cells and seq_center

    Alison Meynert committed Oct 11, 2022
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  4. Prettier & PythonBlack checks

    Alison Meynert committed Oct 11, 2022
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  5. PythonBlack fix

    Alison Meynert committed Oct 11, 2022
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  6. Clarifying that params.seq_center can be overridden by setting seq_ce… 

    …nter in samplesheet
    Alison Meynert committed Oct 11, 2022
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  7. Allows for sequencing center to be set in samplesheet for STARsolo BA… 

    …M file read group info
    Alison Meynert committed Oct 11, 2022
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  8. Prettier fix

    Alison Meynert committed Oct 11, 2022
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  9. Added expected cells to STARsolo via --soloCellFilter

    Alison Meynert committed Oct 11, 2022
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  10. Linting fix

    Alison Meynert committed Oct 11, 2022
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  11. Addition of --expect-cells flag using samplesheet input

    Alison Meynert committed Oct 11, 2022
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  12. Added optional expected cells parameter to cellranger counts process

    Alison Meynert committed Oct 11, 2022
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  13. Linting fixes for spaces

    Alison Meynert committed Oct 11, 2022
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Commits on Oct 12, 2022

  1. autocanceling previous tests when pushing changes

    @kafkasl
    kafkasl committed Oct 12, 2022
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  2. triggering change to test autocancel

    @kafkasl
    kafkasl committed Oct 12, 2022
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  3. updated changelog

    @kafkasl
    kafkasl committed Oct 12, 2022
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  4. Merge pull request #163 from biomage-org/autocancel-old-tests 

    autocanceling previous tests when pushing changes
    @kafkasl
    kafkasl committed Oct 12, 2022
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  5. Added required/optional to samplesheet columns in usage

    Alison Meynert committed Oct 12, 2022
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  6. Fix CI 

    Found by @ameynert right now 🚨
    @apeltzer
    apeltzer committed Oct 12, 2022
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  7. Update ci.yml 

    Fix profile
    @apeltzer
    apeltzer committed Oct 12, 2022
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  8. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Oct 12, 2022
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  9. updated concurrency groups to match nf-core tools

    @kafkasl
    kafkasl committed Oct 12, 2022
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  10. Merge pull request #166 from biomage-org/autocancel-old-tests 

    updated concurrency groups to match nf-core tools
    @kafkasl
    kafkasl committed Oct 12, 2022
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Commits on Oct 13, 2022

  1. Updated simpleaf to version 0.5.3 to allow for expect-cells parameter

    Alison Meynert committed Oct 13, 2022
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  2. Merge pull request #164 from nf-core/params_expansion_150 

    Resolves #150
    ameynert committed Oct 13, 2022
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  3. Add stub for versions.yml in mtx_to_seurat configuration

    @apeltzer
    apeltzer committed Oct 13, 2022
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  4. Merge pull request #165 from nf-core/fix-broken-ci 

    Fix CI
    @apeltzer
    apeltzer committed Oct 13, 2022
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Commits on Oct 17, 2022

  1. Add single-nucleus, RNA velocity option on star.

    @Vivian-chen16
    Vivian-chen16 committed Oct 17, 2022
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Commits on Oct 20, 2022

  1. Adding svg for pipeline picture

    @heylf
    heylf committed Oct 20, 2022
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  2. Adding current version of scrnaseq pipeline picture

    @heylf
    heylf committed Oct 20, 2022
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  3. renaming pipeline picutre

    @heylf
    heylf committed Oct 20, 2022
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  4. Adding future version pipeline picutre

    @heylf
    heylf committed Oct 20, 2022
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  5. Changes to README for pipeline picture

    @heylf
    heylf committed Oct 20, 2022
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  6. Changes to README for pipeline picture

    @heylf
    heylf committed Oct 20, 2022
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  7. Changes to README for pipeline picture

    @heylf
    heylf committed Oct 20, 2022
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  8. initial trial with kallisto exporten t2g

    @kafkasl
    kafkasl committed Oct 20, 2022
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Commits on Oct 24, 2022

  1. Fixing small bug in check_samplesheet

    @heylf
    heylf committed Oct 24, 2022
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  2. Merge pull request #171 from heylf/dev 

    Fixing small bug in check_samplesheet
    @grst
    grst committed Oct 24, 2022
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  3. Merge pull request #169 from heylf/pipe_picture 

    Pipeline picture based on the nf-core best practice pipe-layout
    @grst
    grst committed Oct 24, 2022
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Commits on Oct 25, 2022

  1. Fix prettier block.

    @Vivian-chen16
    Vivian-chen16 committed Oct 25, 2022
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Commits on Oct 28, 2022

  1. Merge pull request #168 from Vivian-chen16/master 

    Add single-nucleus, RNA velocity option on star.
    @Vivian-chen16
    Vivian-chen16 committed Oct 28, 2022
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Commits on Nov 7, 2022

  1. adding gene names to features.tsv for kallisto aligner

    @kafkasl
    kafkasl committed Nov 7, 2022
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Commits on Nov 9, 2022

  1. fix skip_fastqc channel generations

    @fmalmeida
    fmalmeida committed Nov 9, 2022
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  2. added fix info to changelog

    @fmalmeida
    fmalmeida committed Nov 9, 2022
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  3. Merge pull request #179 from nf-core/177-skip_fastqc-argument-leads-t… 

    …o-an-error

fix skip_fastqc channel generations
    @fmalmeida
    fmalmeida committed Nov 9, 2022
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  4. Add Florian Heyl

    @apeltzer
    apeltzer committed Nov 9, 2022
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  5. Add tiny mermaid diagram for existing stuff

    @apeltzer
    apeltzer committed Nov 9, 2022
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  6. change parameter to boolean

    @fmalmeida
    fmalmeida committed Nov 9, 2022
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  7. Adding note for options

    @apeltzer
    apeltzer committed Nov 9, 2022
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  8. adding enabled: params.save_reference to modules that should be affec… 

    …ted by it
    @fmalmeida
    fmalmeida committed Nov 9, 2022
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  9. update changelog

    @fmalmeida
    fmalmeida committed Nov 9, 2022
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  10. added cellranger exports to 10x counts

    @kafkasl
    kafkasl committed Nov 9, 2022
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Commits on Nov 10, 2022

  1. Merge pull request #181 from nf-core/173-should-save_reference-parame… 

    …ter-be-boolean

173 should save reference parameter be boolean
    @apeltzer
    apeltzer committed Nov 10, 2022
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  2. finished star and cellranger

    @kafkasl
    kafkasl committed Nov 10, 2022
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Commits on Nov 11, 2022

  1. Merge branch 'dev' into output-10x-counts

    @kafkasl
    kafkasl committed Nov 11, 2022
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  2. added export_mtx paramter

    @kafkasl
    kafkasl committed Nov 11, 2022
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  3. black formatter

    @kafkasl
    kafkasl committed Nov 11, 2022
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  4. fixed cellranger stub

    @kafkasl
    kafkasl committed Nov 11, 2022
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  5. prettier formatting

    @kafkasl
    kafkasl committed Nov 11, 2022
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  6. fixed other stub

    @kafkasl
    kafkasl committed Nov 11, 2022
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  7. added changelog

    @kafkasl
    kafkasl committed Nov 11, 2022
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Commits on Nov 14, 2022

  1. Update bin/cellranger_mtx_to_h5ad.py 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @kafkasl @grst
    kafkasl and grst committed Nov 14, 2022
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  2. removed --export_mtx and improved kallisto gene name mapping

    @kafkasl
    kafkasl committed Nov 14, 2022
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Commits on Nov 15, 2022

  1. exporting versions in mtx_to_h5ad and unified cellranger w other alig… 

    …ners
    @kafkasl
    kafkasl committed Nov 15, 2022
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  2. run black formatter & prettier

    @kafkasl
    kafkasl committed Nov 15, 2022
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Commits on Nov 17, 2022

  1. Update CHANGELOG.md 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @kafkasl @grst
    kafkasl and grst committed Nov 17, 2022
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  2. Update bin/mtx_to_h5ad.py 

    Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
    @kafkasl @grst
    kafkasl and grst committed Nov 17, 2022
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  3. added task_process name to versions & improved code organization

    @kafkasl
    kafkasl committed Nov 17, 2022
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  4. Merge pull request #160 from biomage-org/output-10x-counts 

    Output 10x counts
    @grst
    grst committed Nov 17, 2022
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Commits on Dec 6, 2022

  1. add UniverSC subworkflow as aligner option

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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  2. set up configuration for UniverSC aligner step

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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  3. add UniverSC to documentation

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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  4. Merge remote-tracking branch 'origin/dev' into universc

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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  5. rename duplicate parameter for index (lint passes)

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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  6. parameter input checks pass with technology as string not file

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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  7. update GitHub Actions to test UniverSC aligner

    @TomKellyGenetics
    TomKellyGenetics committed Dec 6, 2022
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Commits on Dec 8, 2022

  1. Template update for nf-core/tools version 2.7.1

    @nf-core-bot
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Commits on Dec 19, 2022

  1. Template update for nf-core/tools version 2.7.2

    @nf-core-bot
    nf-core-bot committed Dec 19, 2022
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Commits on Feb 13, 2023

  1. Fix 196

    @apeltzer
    apeltzer committed Feb 13, 2023
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  2. Updated black

    @apeltzer
    apeltzer committed Feb 13, 2023
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  3. Merge pull request #197 from nf-core/fix-196 

    Fix 196
    @apeltzer
    apeltzer committed Feb 13, 2023
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Commits on Feb 17, 2023

  1. Adjust simpleaf to use latest simpleaf recipes / containers

    @apeltzer
    apeltzer committed Feb 17, 2023
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  2. Also update alevinqc

    @apeltzer
    apeltzer committed Feb 17, 2023
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  3. Merge branch 'fix-191-and-update-to-template' into nf-core-template-m… 

    …erge-2.7.2
    @apeltzer
    apeltzer committed Feb 17, 2023
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  4. Update modules properly

    @apeltzer
    apeltzer committed Feb 17, 2023
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  5. Modules update

    @apeltzer
    apeltzer committed Feb 17, 2023
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  6. Update schema to make lint pass

    @apeltzer
    apeltzer committed Feb 17, 2023
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  7. Another two [skip_ci]

    @apeltzer
    apeltzer committed Feb 17, 2023
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  8. Revert to 1.12.1

    @apeltzer
    apeltzer committed Feb 17, 2023
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  9. Merge pull request #190 from nf-core/nf-core-template-merge-2.7.2 

    Important! Template update for nf-core/tools v2.7.2
    @apeltzer
    apeltzer committed Feb 17, 2023
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  10. Merge pull request #198 from nf-core/fix-191-and-update-to-template

    @apeltzer
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Commits on Feb 27, 2023

  1. update to call UniverSC module nf-core/modules#1706

    @TomKellyGenetics
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  2. Merge branch 'dev' of ssh://github.com/nf-core/scrnaseq into universc 

    Conflicts:
	CHANGELOG.md
    @TomKellyGenetics
    TomKellyGenetics committed Feb 27, 2023
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Commits on Feb 28, 2023

  1. remove trailing spaces from the documentation

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  2. correct syntax errors in UniverSC subworkflow

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  3. correct syntax errors in UniverSC subworkflow

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  4. bundle universc module into pipeline

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  5. update docs to pass linting

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  6. define universc technology variable

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  7. update index for universc

    @TomKellyGenetics
    TomKellyGenetics committed Feb 28, 2023
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  8. Use conda proper packages too

    @apeltzer
    apeltzer committed Feb 28, 2023
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  9. Update modules, fix issues with pyroe hopefully

    @apeltzer
    apeltzer committed Feb 28, 2023
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  10. Merge branch 'dev' into update-and-fix

    @apeltzer
    apeltzer committed Feb 28, 2023
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  11. Duplicate entries due to merge

    @apeltzer
    apeltzer committed Feb 28, 2023
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  12. Typo :-(

    @apeltzer
    apeltzer committed Feb 28, 2023
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  13. Build bump

    @apeltzer
    apeltzer committed Feb 28, 2023
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Commits on Mar 1, 2023

  1. Merge pull request #185 from TomKellyGenetics/universc 

    UniverSC aligner
    @apeltzer
    apeltzer committed Mar 1, 2023
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  2. require txp2gene file when a salmon_index supplied 

    txp2gene is generated as part of the salmon indexing, but if an index is supplied, the file must be supplied manually
    @azedinez
    azedinez committed Mar 1, 2023
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  3. modify assertion error to reflect changes

    @azedinez
    azedinez committed Mar 1, 2023
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  4. tidying up the assertion 

    merging the conditional with the assertion on line 30
    @azedinez
    azedinez committed Mar 1, 2023
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  5. fix ci issue

    @azedinez
    azedinez committed Mar 1, 2023
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  6. fix ci syntax issue

    @azedinez
    azedinez committed Mar 1, 2023
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Commits on Mar 5, 2023

  1. Re-add conda.enabled

    @grst
    grst committed Mar 5, 2023
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  2. Merge pull request #201 from nf-core/update-and-fix 

    Update all modules, fix template points
    @apeltzer
    apeltzer committed Mar 5, 2023
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  3. Merge pull request #202 from azedine-healx/patch-1 

    fix txp2gene retrieval bug when salmon_index is supplied
    @grst
    grst committed Mar 5, 2023
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Commits on Mar 9, 2023

  1. Fix Seurat container

    @grst
    grst committed Mar 9, 2023
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  2. Update Changelog

    @grst
    grst committed Mar 9, 2023
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  3. Merge pull request #204 from nf-core/fix-193 

    Fix Seurat container
    @grst
    grst committed Mar 9, 2023
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  4. Update modules

    @grst
    grst committed Mar 9, 2023
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  5. Fix linting

    @grst
    grst committed Mar 9, 2023
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  6. try fix linting

    @grst
    grst committed Mar 9, 2023
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Commits on Mar 10, 2023

  1. Merge pull request #205 from nf-core/update-modules 

    Update modules
    @grst
    grst committed Mar 10, 2023
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  2. bump version

    @fmalmeida
    fmalmeida committed Mar 10, 2023
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  3. Merge pull request #206 from nf-core/bump-version 

    bump version
    @fmalmeida
    fmalmeida committed Mar 10, 2023
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Commits on Mar 13, 2023

  1. Fix README/docs

    @grst
    grst committed Mar 13, 2023
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  2. Merge pull request #207 from grst/update-readme 

    update readme
    @grst
    grst committed Mar 13, 2023
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Commits on Mar 17, 2023

  1. Adding universc to pipeline picture

    @heylf
    heylf committed Mar 17, 2023
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Commits on Mar 20, 2023

  1. Merge pull request #209 from heylf/dev 

    Adding universc to pipeline picture
    @grst
    grst committed Mar 20, 2023
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