FriederikeHanssen
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8a7333c13b
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lower case path
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2021-02-24 09:53:11 +01:00 |
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FriederikeHanssen
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7f6e5d9ab5
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try to make a single test pass on GHA, passes locally
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2021-02-24 09:48:55 +01:00 |
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FriederikeHanssen
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e67515809a
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try to only make paired-end test work, pass locally with conda & docker
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2021-02-23 15:47:16 +01:00 |
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FriederikeHanssen
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bf58948dad
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remove todos, describe in/output
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2021-02-23 15:41:11 +01:00 |
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FriederikeHanssen
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4e9d728108
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allow fq.gz or gastq.gz as in/output
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2021-02-23 15:40:22 +01:00 |
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FriederikeHanssen
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12137d6f3e
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Remove trialing whitespace
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2021-02-23 15:00:21 +01:00 |
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FriederikeHanssen
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e251a3bed5
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Remove todos
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2021-02-23 14:58:09 +01:00 |
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FriederikeHanssen
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13733b2581
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Add beautiful md5sums
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2021-02-23 14:57:07 +01:00 |
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FriederikeHanssen
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5e365d5eff
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Make all these tests pass
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2021-02-23 14:09:46 +01:00 |
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FriederikeHanssen
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25a2a16f2d
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Try to make a single test pass
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2021-02-23 13:34:50 +01:00 |
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FriederikeHanssen
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a0c9777d60
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add seqkit to GHA
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2021-02-23 12:43:30 +01:00 |
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FriederikeHanssen
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312bf85f70
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use reasonable option params
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2021-02-23 11:26:54 +01:00 |
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FriederikeHanssen
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9c51e05125
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remove wrong md5 sums
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2021-02-23 11:25:45 +01:00 |
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FriederikeHanssen
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c7d2bc8d43
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Add tests for different options
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2021-02-23 11:14:51 +01:00 |
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FriederikeHanssen
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ec63f335d5
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Add split2 options
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2021-02-22 22:43:32 +01:00 |
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FriederikeHanssen
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5f9aa7264e
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Add tests
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2021-02-17 17:25:41 +01:00 |
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FriederikeHanssen
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2654c52ed1
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Use list of reads as input, similar to dedup/extract
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2021-02-17 17:15:02 +01:00 |
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FriederikeHanssen
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bedc2972eb
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Add seqkit split2
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2021-02-17 17:09:24 +01:00 |
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Harshil Patel
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4d656c8f5f
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Merge pull request #181 from drpatelh/fixes
Fix tests for iVar variants
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2021-02-17 10:08:57 +00:00 |
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Harshil Patel
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f677a6a05e
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Merge pull request #183 from nf-core/MaxUlysse-patch-1
Update .markdownlint.yml
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2021-02-17 00:20:51 +00:00 |
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Harshil Patel
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67d4dab632
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Merge pull request #182 from drpatelh/rm_build
Remove Conda build ids for all modules
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2021-02-17 00:20:00 +00:00 |
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Maxime Garcia
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4c511757f3
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Update .markdownlint.yml
fix typo
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2021-02-17 01:15:21 +01:00 |
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drpatelh
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d47f9bb909
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@kevinmenden sanity fix
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2021-02-16 23:58:52 +00:00 |
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drpatelh
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dcc580e4fb
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Remove Conda build ids for all modules
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2021-02-16 23:58:23 +00:00 |
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Maxime Garcia
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842173be9f
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Merge pull request #175 from MaxUlysse/master_ISSUE_TEMPLATE
fix: add guidelines to PRs and issues
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2021-02-17 00:36:35 +01:00 |
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MaxUlysse
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ebb6d5de1f
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fix: Apply suggestions from code review
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2021-02-17 00:34:55 +01:00 |
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Harshil Patel
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412172cda6
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Merge pull request #180 from MaxUlysse/master_tabix_bgzip
Replace bcftools/bgzip by tabix/bgzip
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2021-02-16 23:32:23 +00:00 |
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Maxime Garcia
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75d1483417
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Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-17 00:32:06 +01:00 |
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drpatelh
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c6a0976f52
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Fix tests for iVar variants
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2021-02-16 23:29:15 +00:00 |
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MaxUlysse
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596bb18394
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fix: rename file to input and gz, plus fix tests
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2021-02-17 00:28:32 +01:00 |
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Harshil Patel
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a282ecd8c7
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Merge pull request #172 from andersgs/ivar-variant
Add ivar variants
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2021-02-16 23:20:30 +00:00 |
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Harshil Patel
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cf2f0762aa
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Update main.nf
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2021-02-16 23:06:26 +00:00 |
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Harshil Patel
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7c276d2974
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Update tests/software/ivar/variants/main.nf
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2021-02-16 23:01:27 +00:00 |
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Harshil Patel
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27020105aa
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Update tests/software/ivar/variants/main.nf
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2021-02-16 23:00:30 +00:00 |
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Harshil Patel
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de90d371dc
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Update tests/software/ivar/variants/main.nf
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2021-02-16 22:58:38 +00:00 |
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Harshil Patel
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23987bdad0
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Update tests/software/ivar/variants/main.nf
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2021-02-16 22:57:47 +00:00 |
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Harshil Patel
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b07ad23efa
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Merge pull request #179 from MaxUlysse/master_htslib_tabix
Replace bcftools/tabix by tabix/tabix
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2021-02-16 22:30:45 +00:00 |
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Harshil Patel
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4f11064ae2
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Update tests/software/tabix/bgzip/main.nf
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2021-02-16 22:30:06 +00:00 |
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Harshil Patel
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8dd6d1d38a
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Update tests/software/tabix/bgzip/main.nf
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2021-02-16 22:29:13 +00:00 |
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Harshil Patel
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759079796a
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Update .github/filters.yml
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2021-02-16 22:24:49 +00:00 |
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Harshil Patel
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d6d34a4b5b
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Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary
Add gatk/createsequencedictionary
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2021-02-16 22:21:38 +00:00 |
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Harshil Patel
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a6d6c0b973
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Update software/gatk/createsequencedictionary/main.nf
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2021-02-16 22:08:11 +00:00 |
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Harshil Patel
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7c64e70c9e
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Update software/gatk/createsequencedictionary/meta.yml
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2021-02-16 22:07:51 +00:00 |
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Harshil Patel
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e558d5fb57
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Merge pull request #174 from andersgs/ivar_consensus_fix
ivar consensus: Add save mpileup as optional in output directive
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2021-02-16 22:04:38 +00:00 |
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Harshil Patel
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d30baa9e54
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Merge pull request #178 from MaxUlysse/master_resource_requirements
Add cpus, memory and time requirements to limit resource consumption
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2021-02-16 22:03:39 +00:00 |
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MaxUlysse
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6a147b8aaa
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chores: replace bcftools/bgzip by tabix/bgzip cf #179
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2021-02-16 19:11:36 +01:00 |
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MaxUlysse
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3805eb2dd1
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fix: remove bcftools/tabix from filters.yml
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2021-02-16 18:38:20 +01:00 |
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MaxUlysse
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5a144d6213
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fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix
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2021-02-16 18:35:32 +01:00 |
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MaxUlysse
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edf5fa3cf6
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fix: merge bcftools/tabix and htslib/tabix into tabix/tabix
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2021-02-16 18:27:13 +01:00 |
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MaxUlysse
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f660324508
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chores: move file
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2021-02-16 18:20:43 +01:00 |
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