Harshil Patel
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eadbea4b83
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Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon
Bowtie2 viralrecon
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2021-01-30 13:22:30 +00:00 |
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sruthipsuresh
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7a1c2a2eb5
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Fixed slop module
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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93e414635b
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Fixed md5sum, fixed filters, fixed slop input
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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78ac4435be
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Added new tests, todo: fix md5sums
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2021-01-29 23:17:44 -06:00 |
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Edmund Miller
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2b0d51ca9c
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test(bedtools): Remove old style tests
AKA how the tests were done last week.
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2021-01-29 23:17:44 -06:00 |
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Edmund Miller
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7d52907d1c
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test(bedtools): Fix typo on yaml indentation
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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ac7f634675
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Added complement test
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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e360617ac6
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Fixed images, genomecov
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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e3bbbb48fc
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Fixed slop file
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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29639c522f
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Corrected sort
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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a108bd407e
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Corrected md5sum and output
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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2f19b4279c
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All modules corrected, TODO config
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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32564137fd
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Corrected workflows and ran editor config
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2021-01-29 23:17:44 -06:00 |
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sruthipsuresh
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672f94f2af
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rebased and updated all bedtools testing and modules
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2021-01-29 23:17:44 -06:00 |
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Harshil Patel
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b260192942
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Merge pull request #149 from heuermh/minimap2
Add minimap2 align module
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2021-02-07 16:37:26 +00:00 |
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Michael L Heuer
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6b873d7d33
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Remove single_end if/else
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2021-02-05 11:35:11 -06:00 |
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Kevin Menden
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17dd0415f2
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Merge pull request #146 from heuermh/bandage
Add bandage image module
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2021-02-05 08:00:44 +01:00 |
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Michael L Heuer
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50bebac136
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Remove pairwise test
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2021-02-04 15:22:12 -06:00 |
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Michael L Heuer
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061b13bf25
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Fix md5 --> md5sum
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2021-02-04 13:48:56 -06:00 |
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Michael L Heuer
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d5f2f5e32d
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Add minimap2 align module
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2021-02-04 13:42:08 -06:00 |
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Michael L Heuer
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37a9f6f456
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Address review comments
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2021-02-04 12:10:54 -06:00 |
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Harshil Patel
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5aa920eb53
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Update tests/software/bowtie/align/test.yml
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2021-02-04 10:19:28 +00:00 |
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Harshil Patel
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68f9a0b711
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Update tests/software/bowtie/build/test.yml
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2021-02-04 10:08:01 +00:00 |
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Harshil Patel
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eb45368a35
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Update tests/software/bowtie2/build/test.yml
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2021-02-04 10:07:44 +00:00 |
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Edmund Miller
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431c699727
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Revert "ci: Test bowtie-build instead of _"
This reverts commit 9b454416d2 .
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2021-02-03 20:06:05 -06:00 |
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Michael L Heuer
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c466255f6f
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Add bandage image module
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2021-02-03 19:31:58 -06:00 |
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Edmund Miller
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9b454416d2
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ci: Test bowtie-build instead of _
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2021-02-03 13:17:14 -06:00 |
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Edmund Miller
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7dbac4bdef
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ci: Test adding another work to test name
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2021-02-03 13:17:14 -06:00 |
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Edmund Miller
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b058da5856
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ci: Test buil to see if build is special
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2021-02-03 12:43:18 -06:00 |
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Edmund Miller
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4d58a037f6
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test(bowtie_align): Fix md5sum
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2021-02-03 12:37:19 -06:00 |
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Edmund Miller
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6901c7e830
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ci: Fix bowtie_build names with ""
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2021-02-03 12:37:14 -06:00 |
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drpatelh
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e71b3eaaa5
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Rename workflows
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2021-02-03 17:48:17 +00:00 |
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drpatelh
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ff6f0642d2
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Fix multiqc tests
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2021-02-03 17:43:14 +00:00 |
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drpatelh
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0683efc679
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Fix salmon quant tests
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2021-02-03 17:36:06 +00:00 |
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drpatelh
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550494cbd1
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Fix picard mergesamfiles test
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2021-02-03 17:31:41 +00:00 |
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drpatelh
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f079ce9d1f
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Fix preseq tests
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2021-02-03 17:28:44 +00:00 |
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drpatelh
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f37fb66f40
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Fix bwa mem tests
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2021-02-03 17:26:43 +00:00 |
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drpatelh
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8a15852756
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Fix salmon index tests
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2021-02-03 17:13:47 +00:00 |
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drpatelh
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058d7b397c
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Fix fastqc test
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2021-02-03 17:03:30 +00:00 |
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drpatelh
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39b8600dbb
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Fix trimgalore test
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2021-02-03 17:02:52 +00:00 |
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drpatelh
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305d47fc87
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Change path to tests
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2021-02-03 16:44:56 +00:00 |
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drpatelh
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a87d584c48
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Change path to bowtie tests
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2021-02-03 16:39:00 +00:00 |
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drpatelh
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9b153f296d
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Add check to see if bowtie bam files exists
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2021-02-03 16:26:10 +00:00 |
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drpatelh
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239cbe17ad
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Fix relative paths
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2021-02-03 16:20:02 +00:00 |
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drpatelh
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38c3ecfac6
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Merge branch 'master' of https://github.com/nf-core/modules into split_tests
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2021-02-03 16:05:06 +00:00 |
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drpatelh
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743ba37d4b
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Update filters paths
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2021-02-03 16:04:43 +00:00 |
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drpatelh
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ff23473e82
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Restructure tests to run individually for each module
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2021-02-03 16:02:58 +00:00 |
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drpatelh
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8be5e05111
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Remove bam md5sum check for bowtie
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2021-02-03 13:46:44 +00:00 |
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drpatelh
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1512c9af74
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Unable to test BAM due to command
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2021-02-03 12:26:10 +00:00 |
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Edmund Miller
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688cc05fe8
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tests: Remove -profile in tests
See ddbca7b467 for more info
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2021-02-02 15:30:59 -06:00 |
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Harshil Patel
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e7b1241449
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Merge pull request #120 from nf-core/composite-runs
Universal CI job
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2021-02-02 18:26:02 +00:00 |
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JoseEspinosa
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ddbe8055c2
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Adding tests
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2021-01-29 19:31:33 +01:00 |
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Harshil Patel
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bd59706d51
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Merge pull request #118 from heuermh/dsh-bio
Added dsh-bio filter-bed as dsh_filterbed
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2021-01-29 18:15:24 +00:00 |
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Harshil Patel
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0fcbc4233c
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Merge pull request #126 from JoseEspinosa/samtools_viralrecon
Samtools viralrecon
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2021-01-29 18:12:48 +00:00 |
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JoseEspinosa
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720db2bed5
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Fixing samtools_mpileup test
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2021-01-29 18:21:03 +01:00 |
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JoseEspinosa
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22dcdc692d
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Adding samtools_mpileup module
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2021-01-29 17:58:42 +01:00 |
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JoseEspinosa
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3eedca9bb4
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Add samtools_view
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2021-01-29 17:18:45 +01:00 |
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kevinmenden
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e8bd730164
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added quast tests
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2021-01-29 16:14:33 +01:00 |
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kevinmenden
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10bb80743a
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started adding quast modules
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2021-01-29 16:06:14 +01:00 |
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kevinmenden
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bacebdfb47
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added pangolin workf
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2021-01-29 12:53:51 +01:00 |
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kevinmenden
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44df90a795
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Merge branch 'master' of https://github.com/nf-core/modules into pangolin-module
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2021-01-29 12:50:24 +01:00 |
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Harshil Patel
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5da41ecb26
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Merge pull request #122 from KevinMenden/master
Added tests and meta.yml files for Salmon
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2021-01-29 11:49:03 +00:00 |
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kevinmenden
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9156becd19
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changed 'covid' to 'sarscov2'
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2021-01-29 12:45:21 +01:00 |
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kevinmenden
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14ade8060f
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added preliminary pangolin test
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2021-01-29 11:12:22 +01:00 |
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kevinmenden
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d91cd73e52
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added test workflow
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2021-01-29 09:41:24 +01:00 |
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kevinmenden
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0780155dc4
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added cutadapt module and tests
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2021-01-29 09:33:45 +01:00 |
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kevinmenden
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3390f7621d
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removed should_exist tag
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2021-01-27 16:32:04 +01:00 |
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kevinmenden
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48c570d6ac
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added file exist to test.yml
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2021-01-27 08:56:25 +01:00 |
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kevinmenden
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431a2eb73b
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added quant test workflow
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2021-01-26 15:58:22 +01:00 |
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kevinmenden
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915e0574a2
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added salmon index test workflow
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2021-01-26 15:44:22 +01:00 |
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kevinmenden
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81bcf0da82
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added test.yml and md5sums
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2021-01-26 15:38:56 +01:00 |
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kevinmenden
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8d4b71355e
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added test data and salmon tests
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2021-01-26 15:24:06 +01:00 |
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kevinmenden
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5be1598b29
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remove log.progress.out from test
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2021-01-25 15:21:48 +01:00 |
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kevinmenden
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a1e1e27f67
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updated test md5sums
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2021-01-25 15:00:18 +01:00 |
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kevinmenden
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71e0de733c
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adapdted star for mutliple output BAMs
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2021-01-25 14:09:03 +01:00 |
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kevinmenden
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6444af7b36
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star module tests
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2021-01-25 09:02:03 +01:00 |
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Edmund Miller
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cff3ac7e5f
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ci: Make an edit to test pipeline trigger
Plus this got clean up in 0c9f29e0a2
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2021-01-24 10:37:29 -06:00 |
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kevinmenden
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f58c1c1e9e
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added star genomegenerate test
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2021-01-22 14:01:59 +01:00 |
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Michael L Heuer
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23f9284aae
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Added dsh-bio split-bed as dsh_splitbed
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2021-01-21 16:34:49 -06:00 |
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Michael L Heuer
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eb6408f3dc
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Added dsh-bio filter-bed as dsh_filterbed
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2021-01-21 15:16:20 -06:00 |
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Edmund Miller
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daa25b9329
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Merge branch 'preseq_test'
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2021-01-15 17:41:13 -06:00 |
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Edmund Miller
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86850dc8a4
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style: Remove old comment
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-01-15 10:32:20 -06:00 |
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sruthipsuresh
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7729fee5a9
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Added gffread and gff3 file for testing
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2021-01-15 10:32:20 -06:00 |
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Edmund Miller
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d7a78fa127
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style: Fix indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-01-15 10:28:11 -06:00 |
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sruthipsuresh
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b95bd37780
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Added ucsc module
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2021-01-15 10:28:11 -06:00 |
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Harshil Patel
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27dbe8b52a
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Merge pull request #115 from Functional-Genomics-Lab/stringtie_test
Added testing for Stringtie
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2021-01-15 16:09:39 +00:00 |
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Edmund Miller
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53830e05c7
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test: Fix typo
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-01-15 10:07:44 -06:00 |
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Edmund Miller
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fe39c7822f
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style: Fix indentation
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2021-01-15 10:01:02 -06:00 |
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Edmund Miller
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b9e8f959b3
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style: Standardize process names
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-01-15 10:00:40 -06:00 |
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sruthipsuresh
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ec91171152
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Corrected naming to ensure test checks work
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2021-01-15 09:38:13 -06:00 |
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sruthipsuresh
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5a1c1f90e5
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removed md5sums for pdf, rdata
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2021-01-15 09:38:13 -06:00 |
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sruthipsuresh
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3f814d1e2f
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Workflow and md5sums added
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2021-01-15 09:38:13 -06:00 |
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sruthipsuresh
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269d9888fe
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Corrected bash error, tested process
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2021-01-15 09:38:13 -06:00 |
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Sruthi Suresh
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b7435b0159
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added test file for phantompeakqualtools for testing
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2021-01-15 09:38:13 -06:00 |
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sruthipsuresh
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09d56efe12
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Fixed with mr file for size issues
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2021-01-14 02:12:57 -06:00 |
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sruthipsuresh
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00ef1d3863
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Changed input to bed files
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2021-01-15 16:52:17 -06:00 |
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sruthipsuresh
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a66618be98
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Delete tests/software/phantompeakqualtools directory
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2021-01-13 21:23:02 -06:00 |
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sruthipsuresh
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6f3cbfcd9a
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Fixed test.yml
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2021-01-12 18:14:28 -06:00 |
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sruthipsuresh
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b297f7aea1
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Fixed test and removed phantompeak tests
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2021-01-12 18:04:12 -06:00 |
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sruthipsuresh
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7c88cf4f67
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Finished module with md5sums
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2021-01-12 09:29:31 -06:00 |
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