Anders Goncalves da Silva
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3188b8e30e
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Add explicit gff is false param
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:55:34 -08:00 |
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Anders Goncalves da Silva
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ee4c2828a0
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Update gff assignment to string
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:55:12 -08:00 |
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Anders Goncalves da Silva
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39401ccd07
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Add gff as input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:54:36 -08:00 |
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Anders Goncalves da Silva
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8b6989f2d7
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Add gff as input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:54:19 -08:00 |
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Anders Goncalves da Silva
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4f8ab8bd69
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Rename gff to features
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:53:30 -08:00 |
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Anders Goncalves da Silva
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8c483d4c6a
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Add gff as input for proper staging
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:53:13 -08:00 |
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Anders Goncalves da Silva
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6259b72081
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Fix output format
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:52:30 -08:00 |
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Anders Goncalves da Silva
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ef1e1b2539
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Fix indentation
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-15 19:51:45 -08:00 |
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Anders Goncalves da Silva
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f841483a70
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Fix URL for containers
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2021-02-15 13:23:35 -08:00 |
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Anders Goncalves da Silva
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9a5aa0f145
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Fix tests to work with gff param
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2021-02-15 11:51:04 -08:00 |
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Anders Goncalves da Silva
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e8d1171b5d
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Make gff a param and not an optional input
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2021-02-15 11:50:52 -08:00 |
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Anders Goncalves da Silva
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4af7414419
|
Add tests for ivar variants
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2021-02-15 09:29:40 -08:00 |
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Anders Goncalves da Silva
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9e3c4e598c
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Add meta to ivar variants
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2021-02-15 09:29:10 -08:00 |
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Anders Goncalves da Silva
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4ab3ccc905
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Add ivar variants
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2021-02-15 09:28:10 -08:00 |
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Anders Goncalves da Silva
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2fe3210f88
|
Add ivar variants
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2021-02-15 09:27:59 -08:00 |
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Harshil Patel
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3d53917b47
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Merge pull request #170 from andersgs/ivar_trim
Add ivar trim
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2021-02-13 08:24:12 +00:00 |
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Harshil Patel
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4af9417b6d
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Update software/ivar/trim/main.nf
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2021-02-13 08:20:06 +00:00 |
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Harshil Patel
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a5686ed14e
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Update software/ivar/trim/main.nf
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2021-02-13 08:19:55 +00:00 |
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Harshil Patel
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f51f8c6400
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Update tests/software/ivar/trim/main.nf
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2021-02-13 08:18:32 +00:00 |
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Harshil Patel
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9d6f29fc61
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Update tests/software/ivar/trim/main.nf
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2021-02-13 08:17:15 +00:00 |
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Harshil Patel
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25f3d46f68
|
Update software/ivar/trim/meta.yml
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2021-02-13 08:17:03 +00:00 |
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Harshil Patel
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cdd9be0a2d
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Update tests/software/ivar/trim/main.nf
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2021-02-13 08:16:44 +00:00 |
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Anders Goncalves da Silva
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bbdca4fa76
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Fix output files
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2021-02-12 16:14:46 -08:00 |
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Anders Goncalves da Silva
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47670a12ad
|
Fix ivar trim test.yml
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2021-02-12 16:03:18 -08:00 |
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Anders Goncalves da Silva
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ed74d366bf
|
Clean up ivar trim main.nf
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2021-02-12 16:03:07 -08:00 |
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Anders Goncalves da Silva
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7c9766962d
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Add ivar trim meta.yml
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2021-02-12 16:02:48 -08:00 |
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Anders Goncalves da Silva
|
6dca7799e6
|
Add ivar trim
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2021-02-12 16:02:10 -08:00 |
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Harshil Patel
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63a20e7b5c
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Merge pull request #168 from JoseEspinosa/bcftools_merge
Add bcftools merge module
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2021-02-12 23:20:30 +00:00 |
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Harshil Patel
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b74ba0af1e
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Merge pull request #162 from andersgs/ivar-consensus
Add ivar consensus module
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2021-02-12 23:18:57 +00:00 |
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Harshil Patel
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c0d128fd39
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Update software/bcftools/merge/main.nf
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2021-02-12 23:16:52 +00:00 |
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Anders Goncalves da Silva
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9268851cde
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Remove samtools option
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-12 15:09:50 -08:00 |
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Anders Goncalves da Silva
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1f66954180
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Relabel input parameter
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2021-02-12 15:09:35 -08:00 |
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JoseEspinosa
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5313698705
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Add bcftools merge module
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2021-02-13 00:08:57 +01:00 |
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Harshil Patel
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96d3b0a18b
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Update tests/software/ivar/consensus/main.nf
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2021-02-12 23:02:25 +00:00 |
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Harshil Patel
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f8916060f8
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Update tests/software/ivar/consensus/main.nf
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2021-02-12 23:02:19 +00:00 |
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Harshil Patel
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0580fd8ded
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Update software/ivar/consensus/main.nf
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2021-02-12 23:02:04 +00:00 |
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Harshil Patel
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9e4539473e
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Update software/ivar/consensus/main.nf
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2021-02-12 23:01:53 +00:00 |
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Harshil Patel
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bc5e073cdb
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Update software/ivar/consensus/main.nf
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2021-02-12 22:57:06 +00:00 |
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Anders Goncalves da Silva
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cb19c7b056
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Fix trailing whitespace
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2021-02-12 14:46:13 -08:00 |
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Anders Goncalves da Silva
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b08bf1ea5c
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Remove ref to conda build and additional params
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2021-02-12 14:43:50 -08:00 |
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Anders Goncalves da Silva
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ffc849761d
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Edit test to output mpileup and passing args to samtools
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2021-02-12 14:43:19 -08:00 |
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Anders Goncalves da Silva
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487ec7b793
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Fix test.yml
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2021-02-12 14:42:42 -08:00 |
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Anders Goncalves da Silva
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24b212318b
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Merge branch 'master' into ivar-consensus
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2021-02-12 11:51:24 -08:00 |
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Anders Goncalves da Silva
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bfc13d3379
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Add options to make samtools more flexible
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2021-02-12 11:50:33 -08:00 |
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Anders Goncalves da Silva
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8b3c16a518
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Add ref FASTA to test main.nf
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2021-02-12 11:29:16 -08:00 |
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Anders Goncalves da Silva
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0a6e8400ac
|
Add reference SC2 genome to test data
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2021-02-12 11:27:12 -08:00 |
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Anders Goncalves da Silva
|
a4bba006bd
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Add reference fasta as input
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2021-02-12 11:26:55 -08:00 |
|
Anders Goncalves da Silva
|
6b22bb9782
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Add meta.yml
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2021-02-12 11:25:40 -08:00 |
|
Anders Goncalves da Silva
|
e5a3e3a5b8
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Add ivar consensus to filter.yml
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2021-02-12 10:59:46 -08:00 |
|
Harshil Patel
|
0b5b8957f4
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Merge pull request #167 from JoseEspinosa/cat_fastq
Add cat fastq module
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2021-02-12 18:02:10 +00:00 |
|