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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5d95151f54
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Fix staging
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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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Moritz E. Beber
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17a9493e6d
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fix: remove typo
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1 year ago |
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Moritz E. Beber
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70dd7cade9
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feat: introduce sample batches for krakenuniq
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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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b3e602dcb3
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Merge branch 'dev' into replace-exit-with-error
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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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sofstam
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c47b9e55fa
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Mix reads in emit
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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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sofstam
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8745fc625c
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Correct output file from samtools/fastq
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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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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 Fellows Yates
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74bc6b7dd3
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Logical ordering and improved commenting
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1 year ago |
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James Fellows Yates
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68d131af34
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Remove leftover dump
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1 year ago |
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James Fellows Yates
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f9af0040bf
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Add multi-run meta information
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1 year ago |
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James Fellows Yates
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e49668005f
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Update docs based on feedback and add missing results directories
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1 year ago |
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James A. Fellows Yates
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5e400c8c89
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Apply suggestions from code review
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1 year ago |
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Moritz E. Beber
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bb7323e25d
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fix: restore setting id on FASTQ meta
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1 year ago |
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Moritz E. Beber
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7104b12e3b
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Update subworkflows/local/longread_preprocessing.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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1 year ago |
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Moritz E. Beber
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fa1c779536
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fix: insert `id` key again
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1 year ago |
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Moritz E. Beber
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246da8a7b0
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chore: remove fixme comments
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1 year ago |
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Moritz E. Beber
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7c1133efb8
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add more comments and slight style changes
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1 year ago |
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Moritz E. Beber
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5380bc18ec
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fix: channels should match 1:1 without remaining elements
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1 year ago |
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Moritz E. Beber
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07db3c93e2
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style: use map addition instead of cloning
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1 year ago |
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Moritz E. Beber
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d17dce5590
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style: use subMap and early returns
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1 year ago |
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Moritz E. Beber
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0bcea6c993
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style: use parameter for branch closure
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1 year ago |
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Moritz E. Beber
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b90433f3c2
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style: use parameters for filter closure
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1 year ago |
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Moritz E. Beber
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aa2410a871
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style: use named parameters for closure
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1 year ago |
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Moritz E. Beber
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c2ad421051
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refactor: simplify DB validation
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1 year ago |
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James Fellows Yates
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98bc6910d5
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Update authors and remove left over comment
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1 year ago |
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James Fellows Yates
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6e64c2b5a9
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Fix copy paste error
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1 year ago |
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James Fellows Yates
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735212c9ee
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Fix the non-updated KAIJU2TABLE name
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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 A. Fellows Yates
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32c0d8d6a5
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Fix KrakenUniq Taxpasta issue
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1 year ago |
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sofstam
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90aa7551a9
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Fix the motus_versions
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1 year ago |
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sofstam
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3fa1b0c17d
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Remove standardised_tables
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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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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 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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b3837cce5b
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Relax strictness so can supply empty db_params but block if only single parameter with out ;
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1 year ago |
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James Fellows Yates
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fe3d42ffd7
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Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters
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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 |