James Fellows Yates
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dfb2e02eb3
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Update gunzip
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1 year ago |
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James Fellows Yates
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2e980f1d15
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Update CAT_FASTQ module
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1 year ago |
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James Fellows Yates
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661cfbe012
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Update UNTAR module
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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 Fellows Yates
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0ed110c529
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BUmp Kraken2 nf-core module to prevent huge logs
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1 year ago |
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sofstam
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d6b60643d9
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Prettier
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1 year ago |
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sofstam
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021f5f0a22
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Remove samtools/bam2fq module
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1 year ago |
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sofstam
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a3d077fcbc
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Prettier
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1 year ago |
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sofstam
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102d53bd75
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Subsitute samtools/bam2fq with samtools/fastq
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1 year ago |
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sofstam
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8ecb655952
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Prettier
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1 year ago |
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sofstam
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213f4e4f23
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Updata taxpasta
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1 year ago |
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sofstam
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c94bfb0cf1
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Fix prettier
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1 year ago |
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sofstam
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4dea308c22
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Linting
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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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sofstam
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dad64a688d
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Add documentation for taxpasta module
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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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a993300099
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Tweaks to MultiQC based on full test experiments
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1 year ago |
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James Fellows Yates
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d6fa45b500
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update MultiQC and include latest modules
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1 year ago |
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James Fellows Yates
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e5c6db96c8
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update all modules to make templaite compatible
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1 year ago |
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Sofia Stamouli
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35b296e5fd
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Merge pull request #202 from nf-core/nf-core-template-merge-2.7.2
Important! Template update for nf-core/tools v2.7.2
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1 year ago |
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James Fellows Yates
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612f532fb2
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Bump KrakenUniq version
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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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0bdc119f9c
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Include falco patch
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1 year ago |
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James Fellows Yates
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e31e7d3172
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Update mOTUs to 3.0.3
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1 year ago |
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James Fellows Yates
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3df0a383da
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Update combine bracken outputs to include meta for publishing purposes
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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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8939ce3e20
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Start adding bracken/combinebrackenreports (need smodule update)
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1 year ago |
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James Fellows Yates
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da3d2d96e6
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Fix linting
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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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James Fellows Yates
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d8751787ac
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Update bracken so parameters come directly from database args
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1 year ago |
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James A. Fellows Yates
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a34b240dfc
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Merge pull request #174 from nf-core/malt-update
Update MALT
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1 year ago |
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James A. Fellows Yates
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4f6eb6fd75
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Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
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1 year ago |
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Moritz E. Beber
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af8ce2cbfd
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chore: update krakenuniq
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1 year ago |
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James Fellows Yates
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9feb6c2db6
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Update MALT
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2 years ago |
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James A. Fellows Yates
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bc671c547d
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Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict
Fix porechop conflict
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2 years 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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3faea8aac5
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Fix porechop conflict
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2 years ago |
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Mahwash Jamy
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3147a80a56
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Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module
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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 |
|
Mahwash Jamy
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86ca71cfd4
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include krakenuniq in profiling subworkflow
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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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4352d35937
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chore: install Bracken module
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2 years ago |
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James Fellows Yates
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56bae85755
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Remove necessity of patch
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2 years ago |