PR for Release 2.0.0 #105
PR for Release 2.0.0 #105
Commits on Feb 18, 2021
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Merge pull request #55 from KevinMenden/dev
DSL2 version with working alevin workflow
Commits on Apr 21, 2021
Commits on Apr 26, 2021
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Merge pull request #57 from maxulysse/dev
Remove social preview image to use GitHub OpenGraph
Commits on Apr 27, 2021
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Apply suggestions from code review
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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Merge pull request #56 from KevinMenden/dev
Added kallistobustools
Commits on Apr 29, 2021
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Commits on Jul 27, 2021
Commits on Oct 22, 2021
Commits on Oct 28, 2021
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Merge pull request #62 from KevinMenden/dev
Update to new file structure
Commits on Oct 29, 2021
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Merge branch 'TEMPLATE' of https://github.com/nf-core/scrnaseq into m…
…erge-template-update
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Merge branch 'dsl2' of https://github.com/nf-core/scrnaseq into merge…
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Merge pull request #74 from ggabernet/merge-template-update
Merge template update v2.1
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Update modules/local/kallistobustools_count.nf
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Commits on Nov 2, 2021
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Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Commits on Dec 14, 2021
Commits on Dec 15, 2021
Commits on Dec 30, 2021
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The report filename was overwritten in case of multiple samples. Also, due to an outdated container image, fonts were not rendered properly in the plots within the report.
Commits on Jan 3, 2022
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Merge pull request #77 from grst/fix-kallistobus
Fix kallistobus didn't run with multiple samples
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Commits on Jan 5, 2022
Commits on Jan 7, 2022
Commits on Jan 12, 2022
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Merge pull request #76 from nf-core/nf-core-template-merge-2.2
All green - lets go!
Commits on Jan 17, 2022
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WIP refactor workflows into subworkflows
There are already some redunancies between the different "workflows" (salmon/alevin/star). This will be getting worse as additional features downstream of the quantification are getting implemented (e.g. conversion to AnnData, ambient RNA filtering etc.) This is the beginning of a series of commits that will turn the workflows into subworkflows: - [ ] Streamline parameter validation and move to main workflow - [ ] Make the different alignment workflow subworkflows that are independent of `params` and get all input values via `take` instead - [ ] Make cellranger subworkflow available
Commits on Jan 20, 2022
Commits on Jan 26, 2022
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Merge pull request #87 from grst/cellranger
Refactor workflows into subworkflows
Commits on Feb 21, 2022
Commits on Mar 15, 2022
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Commits on Mar 24, 2022
Commits on Mar 31, 2022
Commits on May 16, 2022
Commits on May 23, 2022
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input check has a new parameter
Input check has a new parameter that allows the merging ("appending") of reads in the python dictionary only when cellranger is used ... as this problem we were facing only when using it.
Commits on May 27, 2022
Commits on May 30, 2022
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reverted script to allow the use of techinal replicates for all aligners if a sample is defined multiple times, it will only append the file to the dictionary instead of raising an error
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Update kallistobustools_count.nf
instead of using only the first elements of the input array, it now joins the filenames in a single string usig whitespaces. This would make it possible to use it when more replicates are available We may want to add a checking so it complains when not using paired end data.
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added a comment explaining why this channel mapping is still necessary
Commits on May 31, 2022
Commits on Jun 2, 2022
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flattens reads array as it is expected my the module
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Commits on Jun 3, 2022
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Revert "executed prettier on files" as it broke linting
This reverts commit 5c2a21a.
Commits on Jun 7, 2022
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Merge pull request #90 from grst/cellranger2
Integrate cellranger workflow
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Commits on Jun 8, 2022
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Merge pull request #101 from nf-core/nf-core-template-merge-2.4
Important! Template update for nf-core/tools v2.4
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Merge pull request #102 from nf-core/fix-lint
Fix Lint & Update latest modules
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Started working on full-test profile, needs proper human reference + gtf now though
Commits on Jun 9, 2022
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Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
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Merge pull request #103 from nf-core/full-test
Add AWS Full Size Tests
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Commits on Jun 10, 2022
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Merge pull request #97 from truwl/dev
transcriptome_fasta -> transcript_fasta
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Merge pull request #106 from ggabernet/dev
AWS test all profiles and fix publishdir
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add default to outdir as it was in schema
`params.outdir` had a default in schema but not in `nextflow.config`, thus was raising error when user did not specify it.
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Merge pull request #108 from nf-core/fmalmeida-outdir-default
add default to outdir as it was in schema
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Merge pull request #109 from nf-core/fix-full-tests
Fixes full tests with 10x references
Commits on Jun 16, 2022
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Merge pull request #112 from ggabernet/dev
update CI and full size test
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Merge pull request #111 from nf-core/removing-repeatitions
Update nextflow.config
Commits on Jun 17, 2022
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Merge pull request #113 from nf-core/fix-for-60
Fix for STAR chemistry issue #60