PR for Release 2.4.0 #446

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apeltzer merged 414 commits intomasterfrom dev

Oct 14, 2024

+19,101-4,457

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Commits on Sep 5, 2024

Commits on Sep 6, 2024

update docs
atrigila
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fastp3 fix
zxBIB Schcolnicov
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Pulled from dev
zxBIB Schcolnicov
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update tests
atrigila
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Added nftest
zxBIB Schcolnicov
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Merge pull request #412 from nschcolnicov/nextflex
nschcolnicov
authored
Update main.nf
nschcolnicov
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update ci tests nextflex
atrigila
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Commits on Sep 7, 2024

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optionally emit fastq
atrigila
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add metamap
atrigila
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migrate contamination filter to nf-core modules
atrigila
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add config for contamination
atrigila
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remove unused local module
atrigila
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remove dumps
atrigila
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Merge remote-tracking branch 'origin/dev' into nf-core_bowtie_align
atrigila
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update tests
atrigila
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update tests and changelog
atrigila
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Merge pull request #439 from nschcolnicov/issue_415
nschcolnicov
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Merge remote-tracking branch 'origin/dev' into nf-core_bowtie_align
atrigila
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update changelog
atrigila
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Added info about read number behavior
zxBIB Schcolnicov
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Remove trailing space
zxBIB Schcolnicov
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Ran precommit
nschcolnicov
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Updated mirna_quant
zxBIB Schcolnicov
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Updated genome_quant and config
zxBIB Schcolnicov
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Commits on Sep 26, 2024

Merge pull request #441 from atrigila/nf-core_bowtie_align
apeltzer
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Merge pull request #442 from nschcolnicov/issue_94
apeltzer
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Update README.md
apeltzer
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Updated snap tool versions
zxBIB Schcolnicov
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Merge branch 'dev' of https://github.com/nf-core/smrnaseq into migrate_bowtie
zxBIB Schcolnicov
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Merge pull request #444 from nschcolnicov/migrate_bowtie
apeltzer
authored
Merge pull request #445 from nf-core/add-credits
apeltzer
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General cleanup
zxBIB Schcolnicov
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Pre-commit
nschcolnicov
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CHanges in mirdeep and updated bowtie_index channel description
zxBIB Schcolnicov
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erge branch 'issue_400' of https://github.com/nschcolnicov/smrnaseq into issue_400
zxBIB Schcolnicov
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add nf-core mirdeep
atrigila
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add nf-core mirdeep2
atrigila
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update tests
atrigila
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add mirdeep test
atrigila
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update config
atrigila
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update docs
atrigila
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make has fasta/index explicit for mirdeep
atrigila
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Revert "make has fasta/index explicit for mirdeep"
atrigila
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update changelog
atrigila
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remove local unused modules
atrigila
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Revert "remove local unused modules"
atrigila
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Commits on Sep 27, 2024

remove local mirdeep
atrigila
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Merge pull request #448 from atrigila/add_mirdeep_sbwf
atrigila
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Pulled from dev
zxBIB Schcolnicov
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renamed missing variables
zxBIB Schcolnicov
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Commits on Sep 30, 2024

Addressing PR comments
nschcolnicov
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Updated datatable module nftest
nschcolnicov
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Addressing PR comments
zxBIB Schcolnicov
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Merge pull request #447 from nschcolnicov/issue_400
apeltzer
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Removed untar, updated bowtie_channel
zxBIB Schcolnicov
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update tests
atrigila
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Commits on Oct 2, 2024

Commits on Oct 3, 2024

Update usage.md
nschcolnicov
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Commits on Oct 4, 2024

Commits on Oct 5, 2024

Merge pull request #463 from nf-core/update-software-modules
apeltzer
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Commits on Oct 7, 2024

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