James A. Fellows Yates
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ea76a97d99
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Merge branch 'dev' into post-patch-update
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1 year ago |
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James Fellows Yates
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2263d96e73
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Merge remote-tracking branch 'origin/master' into post-patch-update
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1 year ago |
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James Fellows Yates
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982fba1b58
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Fix taxpasta not receiving taxonomy directory
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1 year ago |
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James A. Fellows Yates
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bca6e645a8
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Merge branch 'dev' into nf-core-template-merge-2.8
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1 year ago |
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nf-core-bot
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ac60d66956
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Template update for nf-core/tools version 2.8
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1 year ago |
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James A. Fellows Yates
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ee76a5f38b
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Update conf/modules.config
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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1 year ago |
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James Fellows Yates
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31e3c21dcb
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Make all saveAs conditions consistent
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1 year ago |
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James Fellows Yates
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5d90c775e9
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Logic safety!
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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 Fellows Yates
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94e88d788d
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Everywhere account when no-runmerging for single libs
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1 year ago |
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James Fellows Yates
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e5e0aab59d
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More tweaks
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1 year ago |
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James Fellows Yates
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ca9c0cf8fd
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Further fixes
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1 year ago |
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sofstam
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e274823f73
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Add conf for samtools/fastq
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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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3b90064ba4
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Start adding conditions in modules.conf - non-cat not working
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1 year ago |
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James A. Fellows Yates
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142ff2f099
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Apply suggestions from code review
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1 year ago |
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James Fellows Yates
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577d270423
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Deactivate saving of reads and other large files for full tests
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1 year ago |
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James Fellows Yates
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8ca9fad3b1
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move errorStrategy to config
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1 year ago |
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James Fellows Yates
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b5a2983c5f
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Make modules entries consistent
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1 year ago |
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James Fellows Yates
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a5138ed6e0
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Fix ugly warn when KAIJU2TABLE not run
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1 year ago |
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James A. Fellows Yates
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6c2ce4a1c9
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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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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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Sofia Stamouli
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d96e0a17a5
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Update conf/modules.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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1 year ago |
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sofstam
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2f0c68a833
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Last review suggestions
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1 year ago |
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sofstam
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a7ae57c94e
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Fix linting
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1 year ago |
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sofstam
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e18e68faa5
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Apply review suggestion
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1 year ago |
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sofstam
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5dc3cbc278
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Rename taxonomy argument
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1 year ago |
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sofstam
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5a6fcf1f42
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Update taxpasta/merge to version 0.2.0 and add taxonomy argument
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1 year ago |
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James A. Fellows Yates
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9847b8d9a7
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Fix label base.config for MEGAN_RMA2INFO
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1 year ago |
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sofstam
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04bc978ef6
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Remove taxonomy parameter from taxpasta
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1 year ago |
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sofstam
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90a5668007
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run_malt false in test and add text in output.md
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1 year ago |
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sofstam
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f0aa89cb87
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Rename taxpasta parameters and remove samplesheet parameter
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1 year ago |
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sofstam
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27b7171b96
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Apply review suggestions
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1 year ago |
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sofstam
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2456038567
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Merge branch 'dev' into add_taxpasta_merge
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1 year ago |
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sofstam
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de6a4214ef
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Add taxpasta_merge to taxprofiler
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1 year ago |
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James Fellows Yates
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7dfcdd015b
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Re-add the 'native' combined kaiju output
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1 year ago |
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James Fellows Yates
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79b4db9a34
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Move kaiju2table to profiling
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1 year ago |
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James Fellows Yates
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ce1118930d
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Resource optimisation
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1 year ago |
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James Fellows Yates
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cc7d219267
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Revert "optimisation for single-cpu processes"
This reverts commit a731669b8e.
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1 year ago |
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James Fellows Yates
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a731669b8e
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optimisation for single-cpu processes
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1 year ago |
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James A. Fellows Yates
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45ac6fedc2
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Merge pull request #237 from nf-core/bracken-params
Support Kraken and Bracken db_params in database sheet
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1 year ago |
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James A. Fellows Yates
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70eb84b8d5
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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1 year ago |
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James Fellows Yates
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18886c0cbc
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Start trying a different method with maps in profiling
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1 year ago |
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James Fellows Yates
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059cd17114
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Fix exporting of mapped/unmapped reads for consistency across both short and long reads
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1 year ago |
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sofstam
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5363274867
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Add some last documentation
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1 year ago |
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James Fellows Yates
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7ce55a99e8
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Fix linting
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1 year ago |
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James A. Fellows Yates
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c4e366d47d
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Add full test data and documentation of the test data
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1 year ago |
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James A. Fellows Yates
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1d7da61801
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Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
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1 year ago |
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James A. Fellows Yates
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098ec087c9
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Merge pull request #217 from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
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1 year ago |
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James Fellows Yates
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a993300099
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Tweaks to MultiQC based on full test experiments
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1 year ago |