James A. Fellows Yates
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b299a25bc7
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Merge pull request #286 from nf-core/multiqc-optimisations
MultiQC Optimisations
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1 year ago |
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James A. Fellows Yates
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2140928638
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Merge pull request #272 from nf-core/final-reads-saving
Add 'final reads for profiling' saving mechanism
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1 year ago |
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James A. Fellows Yates
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5a09319fb3
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Merge branch 'dev' into multiqc-optimisations
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1 year ago |
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James Fellows Yates
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1eb951715f
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MultiQC optimisations for DIAMOND and Falco
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1 year ago |
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James A. Fellows Yates
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0245c4880b
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Merge branch 'dev' into final-reads-saving
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1 year ago |
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James A. Fellows Yates
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03c3169f10
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Replace all instance of exit 1 with error for safety and consistency
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1 year ago |
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James Fellows Yates
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6895e45768
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Fix a few conditional bugs and related
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1 year ago |
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James Fellows Yates
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fbecfb6f33
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Fix broken check for host read removal index
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1 year ago |
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James Fellows Yates
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5c549e5ce3
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Remove TODOs and references to under development
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1 year ago |
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James Fellows Yates
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225773000f
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Fix channel structure when supplying own host bt2 index
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1 year ago |
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James Fellows Yates
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cac6f54d2d
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[extra] Fix warn related to recently changed parameter
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1 year ago |
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James Fellows Yates
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ab0c62bdc1
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Post-release tweaks to usage.md
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1 year ago |
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James A. Fellows Yates
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acba31a8d6
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Update taxprofiler.nf
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1 year ago |
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James A. Fellows Yates
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e586747680
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Add missing comma to list
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1 year ago |
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sofstam
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6ebfdcd017
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Add path parameters
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1 year ago |
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Sofia Stamouli
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d691b89727
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Merge branch 'dev' into nf-core-template-merge-2.7.2
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1 year ago |
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James A. Fellows Yates
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25bb4304e8
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Merge pull request #187 from nf-core/revert-pep
Revert PEP validation back to python samplesheet check
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1 year ago |
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nf-core-bot
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ab591e01ff
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Template update for nf-core/tools version 2.7.2
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1 year ago |
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James Fellows Yates
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07bd989bc6
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Start work on groovy native datbase checks
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1 year ago |
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James Fellows Yates
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4b68e95770
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Revert PEP validation back to python samplesheet check
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1 year ago |
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James Fellows Yates
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1ccd0a0767
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Merge branch 'dev' into nf-core-template-merge-2.7.1
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1 year ago |
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nf-core-bot
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36f3b5723b
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Template update for nf-core/tools version 2.7.1
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1 year ago |
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Moritz E. Beber
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4529e7e545
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refactor: change parameter exclude unmerged to include
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1 year ago |
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James A. Fellows Yates
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1f31f88635
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Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
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2 years ago |
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James Fellows Yates
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d487a1ff2f
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Addd FASTP adadapter list
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2 years ago |
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Sofia Stamouli
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1bd6dbfe58
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Add samtools stats for long-reads
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2 years ago |
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Moritz E. Beber
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bf89525bc2
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Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
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2 years ago |
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James A. Fellows Yates
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76a662ecc5
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Fix adapterremoval adapter conflict and add optional adapter list file
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2 years ago |
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Sofia Stamouli
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d3d4297ca9
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Apply review suggestions
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2 years ago |
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Sofia Stamouli
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511cb16a61
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Apply review suggestions
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2 years ago |
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Sofia Stamouli
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8eddb32b88
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Add Falco as an alternative to FastQC
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2 years ago |
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Moritz E. Beber
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8768a16d63
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refactor: turn warning into error
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2 years ago |
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Moritz E. Beber
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fd8a0df2a6
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refactor: add warning when run_kraken2 is missing
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2 years ago |
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Moritz E. Beber
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fdb8a7f740
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Merge branch 'devel' into nf-core-template-merge-2.6
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2 years ago |
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nf-core-bot
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51bacb00e6
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Template update for nf-core/tools version 2.6
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2 years ago |
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Rafal Stepien
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bfd260e9c8
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Update workflows/taxprofiler.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2 years ago |
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Rafal Stepien
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9349346864
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Remove --pep parameter and leave just --input
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2 years ago |
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Rafal Stepien
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768f9980d8
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Add pep_input_base_dir to workflow. Just need to update modules
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2 years ago |
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Rafal Stepien
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5f3eee9a4a
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Add working version of PEP-nf-core integration
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2 years ago |
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James A. Fellows Yates
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cc5df924e4
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Merge branch 'dev' into module-update
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2 years ago |
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James Fellows Yates
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fc26948950
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Fix MultiQC
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2 years ago |
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James Fellows Yates
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d11257b330
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Module update
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2 years ago |
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James Fellows Yates
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bbd8049ca1
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Remove duplicated multqic mixing
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2 years ago |
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James Fellows Yates
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7c5f9d0c24
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Start work on more merging tools
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2 years ago |
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James Fellows Yates
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5552c264b9
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Remove now unnecessary input validation
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2 years ago |
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James Fellows Yates
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8917e29e35
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Fix accidental overly zelous search-and-replace
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2 years ago |
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James Fellows Yates
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3f8f32cba8
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Make longread quality ftilering opt out
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2 years ago |
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James Fellows Yates
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2cc07183a0
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Standardise QC parameter system and turn on both porechop/filtlong in tests
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2 years ago |
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James Fellows Yates
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139cf0d6aa
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Fix
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2 years ago |
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James A. Fellows Yates
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cc3967a3fd
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Apply suggestions from code review
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2 years ago |