James Fellows Yates
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564474cafe
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Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.
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2022-04-18 07:21:12 +02:00 |
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James Fellows Yates
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aa2d07c42a
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Fix merge cockup
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2022-04-13 14:19:19 +02:00 |
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James A. Fellows Yates
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70f94603b0
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Merge branch 'dev' into hostremoval
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2022-04-13 13:59:51 +02:00 |
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James Fellows Yates
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dfeaa0d1fe
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Rename subworkflow parameters for consistency
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2022-04-13 12:00:28 +02:00 |
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James Fellows Yates
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16a3556bfc
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Changes after code review
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2022-04-13 08:26:08 +02:00 |
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James Fellows Yates
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2ef21c6ef3
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Fix input to profiling
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2022-04-12 10:14:05 +02:00 |
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James A. Fellows Yates
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967b1f7d6e
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Merge branch 'dev' into run-merging
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2022-04-12 09:28:10 +02:00 |
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James Fellows Yates
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a5f4fc42d5
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Fix run merging for unmerged PE data
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2022-04-12 09:25:27 +02:00 |
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James Fellows Yates
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78182c2a8c
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Add comma
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2022-04-11 13:40:24 +02:00 |
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James A. Fellows Yates
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025083061e
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Merge branch 'dev' into hostremoval
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2022-04-11 13:36:03 +02:00 |
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James Fellows Yates
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030099c559
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A bit of clean up
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2022-04-10 07:26:20 +02:00 |
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James Fellows Yates
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80c08af11b
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Mix in profiling versions into mainline versons channel
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2022-04-10 06:48:25 +02:00 |
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James Fellows Yates
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082093f3de
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Prettier
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2022-04-10 06:44:10 +02:00 |
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James Fellows Yates
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ecf0eea4f9
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Move profiling to subworkflow and standardise outputs
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2022-04-10 06:43:30 +02:00 |
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James Fellows Yates
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afb66e445f
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Append pairment to ID at profiling to prevent multiqc-level filename crash
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2022-04-08 21:36:59 +02:00 |
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James Fellows Yates
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8839fe22b8
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Fix output tuple for reads
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2022-04-08 20:02:22 +02:00 |
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James Fellows Yates
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ca011ccc5b
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Fix cat_fastq naming logic?
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2022-04-08 13:28:37 +02:00 |
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James Fellows Yates
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d130a72d74
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Get this working
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2022-04-08 13:09:23 +02:00 |
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James Fellows Yates
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4d726a87e9
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Fix metadata removal
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2022-04-08 12:01:07 +02:00 |
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James Fellows Yates
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74c496f6af
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Fix CAT_FASTQ output
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2022-04-08 11:58:16 +02:00 |
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James Fellows Yates
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7b08c49cd6
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Re-add run merging and gonna let GHA see if it works >.>
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2022-04-08 11:54:54 +02:00 |
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sofstam
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606e5da7d5
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Check if PR works with centrifuge/centrifuge module
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2022-04-07 16:13:17 +02:00 |
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James A. Fellows Yates
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b554aa3e4d
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Merge branch 'dev' into hostremoval
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2022-04-07 14:00:10 +02:00 |
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James Fellows Yates
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98f082d7b6
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Fix mistake in previous upstream merge with AR2 output channel for settings file
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2022-04-05 13:17:54 +02:00 |
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James Fellows Yates
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5b9355725d
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Whoops
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2022-04-05 13:14:06 +02:00 |
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James Fellows Yates
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245a4d1f5d
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Fix MQC staging and remove debugging dump
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2022-04-05 13:08:44 +02:00 |
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James A. Fellows Yates
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3d662d2e06
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Merge branch 'dev' into complexity-filter-bbduk
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2022-04-04 21:19:36 +02:00 |
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sofstam
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d897c922b2
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Add centrifuge classificatioN
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2022-04-04 13:51:51 +02:00 |
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James A. Fellows Yates
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b2e29ea23a
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Merge branch 'dev' into hostremoval
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2022-04-03 17:24:07 +02:00 |
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James Fellows Yates
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066ceb2bca
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Remove flagstat as bowtie2 reports this itself
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2022-04-03 17:23:14 +02:00 |
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James Fellows Yates
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482112bb42
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Start work on host removal
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2022-04-03 07:58:40 +02:00 |
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James Fellows Yates
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469e4f3682
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Remove remaining debugging .dumps(
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2022-04-02 17:07:30 +02:00 |
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James Fellows Yates
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b055df5ea0
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Add bbduk complexity (entropy-based) filtering
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2022-04-02 17:02:05 +02:00 |
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Moritz E. Beber
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996b3f4912
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fix: correct the input shape to metaphlan3
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2022-04-02 15:00:26 +02:00 |
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Moritz E. Beber
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a425a322f2
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refactor: make metaphlan3 run in workflow
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2022-04-02 14:59:44 +02:00 |
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Moritz E. Beber
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69db920610
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feat: include metaphlan3 in workflow
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2022-04-02 14:59:44 +02:00 |
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James Fellows Yates
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93aaa9eeac
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Clean up AdapterRemoval and remove all debugging dumps
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2022-04-01 21:36:22 +02:00 |
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James Fellows Yates
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94e5cfef4a
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Filter long reads for MALT, bump cpus for FastQC for minigut to pass
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2022-03-28 18:20:10 +02:00 |
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James Fellows Yates
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231253227c
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Remove run merging for now due to complexity
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2022-03-28 16:38:10 +02:00 |
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James Fellows Yates
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ee53283696
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Debugging comment
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2022-03-28 09:13:05 +02:00 |
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James Fellows Yates
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8dc9e583ad
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Debugging run merging
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2022-03-27 09:30:23 +02:00 |
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James A. Fellows Yates
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e6e8ed7cc9
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Add some debugging notes
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2022-03-26 20:54:50 +00:00 |
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James Fellows Yates
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120382f51d
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Fix input channels to kraken2
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2022-03-26 06:45:16 +01:00 |
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sofstam
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37a70dc3e3
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Merge branch 'dev' into classification_centrifuge
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2022-03-25 16:18:35 +01:00 |
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James Fellows Yates
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4e93abc7c0
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Add read improved read preprocessing
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2022-03-25 14:58:06 +01:00 |
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James Fellows Yates
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cc9368ee52
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Prettier linting and update schema
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2022-03-24 15:35:09 +01:00 |
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James A. Fellows Yates
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edce6603ef
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Merge branch 'dev' into nf-core-template-merge-2.3.2
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2022-03-24 14:10:58 +01:00 |
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sofstam
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3ff54e620e
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Add centrifuge classification
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2022-03-24 13:02:25 +01:00 |
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nf-core-bot
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6b939e6728
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Template update for nf-core/tools version 2.3.1
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2022-03-23 13:57:56 +00:00 |
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James Fellows Yates
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81bfb629ca
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Add working basic test to begin
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2022-03-21 20:28:09 +01:00 |
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