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Release - 1.1.0#45

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jannikseidelQBiC merged 127 commits intomasternf-core/detaxizer:masterfrom devnf-core/detaxizer:devCopy head branch name to clipboardNov 8, 2024

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Commits on Apr 4, 2024

• Merge pull request #27 from nf-core/master

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• bumped version to 1.1.0dev

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• Merge pull request #28 from jannikseidelQBiC/post1.0.0versionbump

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Commits on May 8, 2024

• Template update for nf-core/tools version 2.14.0

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• Template update for nf-core/tools version 2.14.1

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Commits on Jun 10, 2024

• Merge branch 'dev' into nf-core-template-merge-2.14.1

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• Update nextflow_schema.json

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• Merge pull request #31 from nf-core/nf-core-template-merge-2.14.1

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Commits on Jun 27, 2024

• fixed bug

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• added bugfix to changelog

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• [automated] Fix code linting

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• changed linked issue to pr in changelog

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• Merge pull request #33 from jannikseidelQBiC/bugfix

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Commits on Aug 6, 2024

• added funding information to readme

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Commits on Aug 8, 2024

• Introduction of bbduk into detaxizer; making blastn optional

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• removal of SUMMARY_KRAKEN2 from modules.config

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• update of modules

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Commits on Aug 13, 2024

• split of fasta parameter into fasta_bbduk and fasta_blastn

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• changed label of bbduk to 'process_high'

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Commits on Aug 14, 2024

• fixed logic for deciding how to process ids

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Commits on Aug 16, 2024

• added dont_eval_duplication to fastp and turned off preprocessing by default

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• adapted meta.id of summary processes to new concept of detaxizer

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• made preprocessing with fastp optional

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• enable optional output of the removed reads

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• introduced optional classification of the filtered (and removed) reads after filtering with kraken2

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• Updated CHANGELOG.md

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• Updated test_full.config

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• added version output of processes to multiqc

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Commits on Aug 19, 2024

• changed kraken2 post classification to be output as default if post-filter classification is enabled

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Commits on Aug 29, 2024

• update kraken2 default database

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• fix: test for blastn was adapted to new reference parameter

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• removed unused parameters for blastn

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• update kraken2 database and alignment of values

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Commits on Aug 30, 2024

• adapted tests

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• removed blastn from standard test

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• default tax2filter to 'Homo sapiens'

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• prettification of modules.json

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• changed behavior of params.preprocessing

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• changed tax2filter in full test to 'Homo sapiens'

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Commits on Sep 2, 2024

• [automated] Fix code linting

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• Update CHANGELOG.md

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Commits on Sep 3, 2024

• fixed indentation

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• removed blank line

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• Update CHANGELOG.md

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• [automated] Fix code linting

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• removal of redundant code in classification step

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• Change of logic for the merging step of the classification to be functional

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• removal of blank line

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• Addition of DZIF to funding information

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Commits on Sep 4, 2024

• Merge pull request #34 from jannikseidelQBiC/feature_bbduk

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• Updated citations

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• Updated README.md

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• Updated detaxizer metro map

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• fixed typo

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• updated usage.md

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• changed output folder of MERGE_IDS process

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• updated output.md

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• updated output.md

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• [automated] Fix code linting

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Commits on Sep 5, 2024

• fixed typos

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• update output.md

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• updated README.md

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• Merge pull request #35 from jannikseidelQBiC/feature_bbduk_docu

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Commits on Oct 8, 2024

• Template update for nf-core/tools version 3.0.0

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Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

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Commits on Oct 10, 2024

• initial setup detaxizer -> taxprofiler

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• fix nanopore logic

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• add docs

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Commits on Oct 11, 2024

• add workflow logic samplesheet generation + function

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• Template update for nf-core/tools version 3.0.2

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Commits on Oct 14, 2024

• add nf-test for subworkflow

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• add support for MAG

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• adding outpath

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• update snapshot with outpath

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• update nf-test use real files & nf-testcsv

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• implement suggestions

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• additional check new input params

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Commits on Oct 15, 2024

• Merge branch 'TEMPLATE' of https://github.com/nf-core/detaxizer into merging-template-updates

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• splitting up PE and SE for samplesheet generation

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• remove unnecesry function call & update tests

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• making to samplesheet function more easy to read

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• update output docs & remove standalone long reads

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Commits on Oct 16, 2024

• updated CHANGELOG.md

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• [automated] Fix code linting

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• setting memory to 15 GB (as intended in the template update)

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• Merge pull request #42 from jannikseidelQBiC/merging-template-updates

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• Merge remote-tracking branch 'origin/dev' into samplesheet-gen-taxprofiler

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• implement reviewer comment

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• fix linting

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Commits on Oct 17, 2024

• Merge pull request #39 from nf-core/samplesheet-gen-taxprofiler

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• Updated changelog

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• Update readme, samplesheet and supported pipelines

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• make the false ci go away

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Commits on Oct 18, 2024

• Merge pull request #43 from nf-core/update-changelog-samplesheet-generation

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Commits on Oct 21, 2024

• update modules

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• update manifest

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• update config description

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• update changelog

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• preparation of release 1.1.0

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• uncomment includeConfig for custom profiles

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• update kraken2 default db

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• fix typo

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• update changelog

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Commits on Oct 22, 2024

• updated release date in changelog

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• Merge pull request #44 from jannikseidelQBiC/preparation-release

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• fixing gzip too many symlink levels error

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Commits on Oct 23, 2024

• Merge pull request #46 from jannikseidelQBiC/fix-gzip-conda

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Commits on Oct 30, 2024

• changed pipeline version and description

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• minor changes in metro map

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• rename meta1 to meta2

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Commits on Oct 31, 2024

• update CHANGELOG.md

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• update README.md

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• update usage.md

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• update output.md

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• remove todo from nextflow.config

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Commits on Nov 1, 2024

• change name of fasta_* channels to follow ch_* convention

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• removing set from channels for consitency (except template channels)

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• remove whitespace

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• changes in usage of whitespace for consitency and readability

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• [automated] Fix code linting

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• removed trailing whitespaces

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• Merge branch 'corrections_release1.1.0_I' of https://github.com/jannikseidelQBiC/nf-core-detaxizer into corrections_release1.1.0_I

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Commits on Nov 4, 2024

• Merge pull request #47 from jannikseidelQBiC/corrections_release1.1.0_I

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Commits on Nov 7, 2024

• update CHANGELOG.md

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• Don't check tests if there are no tests

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• Merge pull request #49 from nf-core/aws-fulltest-manual-fix

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Commits on Nov 8, 2024

• Merge pull request #48 from jannikseidelQBiC/update-release-date-release1.1.0

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