James Fellows Yates
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9880baa0b8
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Get build directory working
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2022-04-18 06:37:23 +02:00 |
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James Fellows Yates
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b036ed5b73
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Prettier
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2022-04-17 22:28:18 +02:00 |
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James Fellows Yates
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2cfcdf2dd2
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Add finer controler over for hostremoval saving
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2022-04-17 22:27:04 +02:00 |
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James A. Fellows Yates
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fc8a83245a
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Add short-read host removal via BowTie2 alignment mapping
Add short-read host removal via BowTie2 alignment mapping
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2022-04-13 15:29:16 +02:00 |
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James A. Fellows Yates
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5e80df0f94
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Apply suggestions from code review
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2022-04-13 15:27:53 +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 A. Fellows Yates
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67d94a9a8d
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Merge pull request #45 from nf-core/run-merging
Re-add run merging
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2022-04-13 12:27:37 +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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a15c45b00c
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Put map in the rigt place
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2022-04-12 10:51:27 +02:00 |
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James Fellows Yates
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8d68914192
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Re-add operator name
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2022-04-12 10:47:44 +02:00 |
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James Fellows Yates
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26399718b2
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Re-add pairment attachment
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2022-04-12 10:46:03 +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 Fellows Yates
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9f221f84cc
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Only supply single input channel to profiling, as these are merged into single input channel at run_merging
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2022-04-12 10:12:17 +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 A. Fellows Yates
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1ac5a129a8
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Merge pull request #52 from genomic-medicine-sweden/delete_extra_directory
Delete extra unnecessary directory
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2022-04-11 20:46:50 +02:00 |
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sofstam
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989dc55ce1
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Delete extra nf-core directory
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2022-04-11 17:42:38 +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 Fellows Yates
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ff2e508a38
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Merge branch 'hostremoval' of github.com:nf-core/taxprofiler into hostremoval
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2022-04-11 13:38:53 +02:00 |
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James Fellows Yates
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29073e3c93
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Update CI tests
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2022-04-11 13:38:42 +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 A. Fellows Yates
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fb2f5ed73e
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Merge pull request #50 from nf-core/docs-prelim
Initial attempt at adding usage docs
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2022-04-11 10:52:18 +02:00 |
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James A. Fellows Yates
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b8b11fd065
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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-04-11 10:30:29 +02:00 |
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James Fellows Yates
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b892fd0be5
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Initial attempt at docs
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2022-04-10 22:17:44 +02:00 |
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James A. Fellows Yates
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dd22e042be
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Merge pull request #47 from nf-core/profiling-subworkflow
Move profiling to subworkflow
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2022-04-10 16:54:35 +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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35cb6e042a
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Flatten the right thing
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2022-04-08 13:46:12 +02:00 |
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James Fellows Yates
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6c14f2b230
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Remove the flattening?
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2022-04-08 13:44:52 +02:00 |
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James Fellows Yates
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a634814d84
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Formatting and fix fastp output
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2022-04-08 13:34:00 +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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Sofia Stamouli
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5f24f94391
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Merge pull request #31 from genomic-medicine-sweden/classification_centrifuge
Add centrifuge classification (centrifuge/centrifuge module)
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2022-04-08 11:26:57 +02:00 |
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Sofia Stamouli
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63bc597daf
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Prettier
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2022-04-08 11:01:45 +02:00 |
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Sofia Stamouli
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fd5ebea9a6
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Remove old centrifuge module
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2022-04-08 10:57:58 +02:00 |
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Sofia Stamouli
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48d28cf8d4
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Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-04-08 10:00:10 +02:00 |
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Sofia Stamouli
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2dfe3b3cc1
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Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-04-08 10:00:04 +02:00 |
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Sofia Stamouli
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3d45ac57ae
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Prettier
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2022-04-07 16:42:22 +02:00 |
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sofstam
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26779a4420
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Remove db_name from nextflow.config
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2022-04-07 16:27:19 +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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