Jose Espinosa-Carrasco
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72e81d6e90
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Add spades module (#277)
* Add spades module
* Reorder gatk4 modules alphabetically
* Update software/spades/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-03-18 13:48:38 +00:00 |
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Jose Espinosa-Carrasco
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313241749c
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Add kraken2 run module (#266)
* Add kraken2 run module
* Add kraken2 run module
* Add coronavirus kraken2 db
* Adding kraken2 run tests
* Update software/kraken2/run/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixing files commited by mistake
* Remove params for meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-03-18 13:08:06 +00:00 |
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Kevin Menden
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a90332906b
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add mergebamalignment (#259)
* add mergebamalignment
* fix test.yml
* update to latest gatk4 version
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/data/README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/meta.yml
* fixed unmapped/unaligned
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-03-17 15:56:56 +01:00 |
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Kevin Menden
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3c4d9466f4
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Adding minia for viralrecon (#267)
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-03-17 12:54:15 +01:00 |
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Kevin Menden
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17dbff52f4
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added gatk4 variantfiltration (#265)
* added gatk4 variantfiltration
* replace merge with filter
* Update software/gatk4/variantfiltration/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* updated input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-03-17 09:42:35 +01:00 |
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Jose Espinosa-Carrasco
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74ff11b07b
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Fix bowtie builds (#273)
* Fix bowtie build test
* Forgot to delete old bowtie_build
* Fix bowtie2 build tests
* Add initOptions include on hisat2 extractsplicesites
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2021-03-15 15:39:42 +01:00 |
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Harshil Patel
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9b99b33401
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Rename .github/filters.yml -> tests/config/pytest_software.yml (#271)
* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
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2021-03-15 12:51:30 +00:00 |
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