James Fellows Yates
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95ad380173
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Turn of length filtering by default for short read (to match opt in for longread qc)
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2022-08-30 14:01:52 +02:00 |
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James Fellows Yates
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2cc07183a0
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Standardise QC parameter system and turn on both porechop/filtlong in tests
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2022-08-30 13:58:58 +02:00 |
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James A. Fellows Yates
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1821496a49
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Merge pull request #90 from nf-core/samplesheet-check-improvement
Make check_samplesheet.py compatible with nf-core/fetchngs
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2022-08-23 15:57:59 +01:00 |
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James A. Fellows Yates
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22e03e73e3
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Merge pull request #111 from nf-core/minimal-test
Add test_nothing config profile for very minimal testing
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2022-08-23 15:57:52 +01:00 |
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James A. Fellows Yates
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a3055bf6da
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Update conf/test_nothing.config
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2022-08-23 15:48:02 +02:00 |
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James A. Fellows Yates
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4315141c5f
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Update bin/check_samplesheet.py
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-08-23 15:44:53 +02:00 |
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James Fellows Yates
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e6c7939305
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Add test_nothing config profile for minimal testing
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2022-08-23 14:37:01 +02:00 |
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James Fellows Yates
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a97bb69cd2
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Prettier
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2022-08-23 14:24:57 +02:00 |
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James A. Fellows Yates
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de70b0a01d
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Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
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2022-07-29 13:36:25 +02:00 |
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James A. Fellows Yates
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3e24f491b5
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Merge pull request #106 from nf-core/porechop-log
Add emitting porechop logs to multiqc and fix collection of others
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2022-07-29 10:58:12 +02:00 |
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James A. Fellows Yates
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f48b22d615
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Apply suggestions from code review
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2022-07-29 09:52:49 +02:00 |
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James Fellows Yates
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873a13e028
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Merge remote-tracking branch 'origin/dev' into porechop-log
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2022-07-29 09:51:34 +02:00 |
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Mahwash Jamy
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06298e867c
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Merge pull request #105 from genomic-medicine-sweden/diamond-update
Update the dev branch with the DIAMOND module update
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2022-07-28 17:21:59 +02:00 |
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mjamy
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5cdf5e958a
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Updated modules.config to add 'log' in diamond config
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2022-07-28 16:08:15 +02:00 |
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Mahwash Jamy
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49487593e2
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Merge branch 'nf-core:dev' into diamond-update
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2022-07-28 15:48:59 +02:00 |
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Sofia Stamouli
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ba928af5ab
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Merge pull request #110 from genomic-medicine-sweden/update_centrifuge_kreport
Update centrifuge kreport
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2022-07-28 10:36:30 +02:00 |
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sofstam
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71cf32cc6a
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Add error strategy for centrifuge/kreport
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2022-07-28 08:54:32 +02:00 |
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sofstam
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9bc45a3f24
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Update centrifuge/kreport
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2022-07-27 14:44:26 +02:00 |
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sofstam
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cecbb41f88
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Update centrifuge/kreport
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2022-07-27 14:42:35 +02:00 |
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James Fellows Yates
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25bcc0798d
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Start work on multiQC config with distinguishing Kraken/Centrifuge
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2022-07-27 14:40:17 +02:00 |
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nf-core-bot
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a3bcf8665a
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[automated] Fix linting with Prettier
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2022-07-26 18:47:40 +00:00 |
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James A. Fellows Yates
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65ae82efc4
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Define separte krakena nd centrigfue modules
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2022-07-26 18:37:33 +00:00 |
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James A. Fellows Yates
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9d2be68fb8
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Merge branch 'dev' into centrifuge_mqc
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2022-07-26 18:01:30 +00:00 |
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James A. Fellows Yates
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1ef0975736
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Merge branch 'dev' into porechop-log
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2022-07-26 18:00:28 +00:00 |
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James A. Fellows Yates
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fdd9a3bc4d
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Merge pull request #107 from nf-core/fix-multiqc-mixing
Fix MultiQC mixing
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2022-07-26 12:38:52 +02:00 |
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James A. Fellows Yates
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65b0af9a8b
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Fix profiling channels
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2022-07-26 08:53:43 +00:00 |
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James A. Fellows Yates
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3054dea7c2
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Get multiqc input working
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2022-07-26 08:41:06 +00:00 |
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James A. Fellows Yates
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e76b299705
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Start working getting kraken and centrifuge working in MQC
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2022-07-26 08:18:54 +00:00 |
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James Fellows Yates
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139cf0d6aa
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Fix
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2022-07-26 10:12:33 +02:00 |
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James A. Fellows Yates
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64f01fcfe0
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Merge branch 'dev' into porechop-log
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2022-07-20 14:05:23 +02:00 |
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Sofia Stamouli
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1fe9c133f1
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Merge pull request #103 from genomic-medicine-sweden/update_filtlong
Update the dev branch with the filtlong update
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2022-07-20 10:44:52 +02:00 |
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James Fellows Yates
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255afee4c7
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Re-add the collects
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2022-07-19 17:10:10 +02:00 |
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Mahwash Jamy
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811ded38af
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Update subworkflows/local/profiling.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-07-19 16:44:48 +02:00 |
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Sofia Stamouli
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237e9aa623
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Update longread_preprocessing.nf
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2022-07-19 16:44:08 +02:00 |
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James A. Fellows Yates
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8d7ddb5847
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Apply suggestions from code review
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2022-07-19 16:30:13 +02:00 |
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mjamy
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c4c82212e1
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incorporate diamond log file into multiqc channel
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2022-07-19 14:12:16 +02:00 |
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sofstam
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171258d545
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Fix typos
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2022-07-19 14:07:13 +02:00 |
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sofstam
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25bc01f9c4
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Fix typos
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2022-07-19 14:04:49 +02:00 |
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sofstam
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8147dba0b4
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Fix typos
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2022-07-19 14:03:10 +02:00 |
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sofstam
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526ed79763
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Fix filtlong logs
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2022-07-19 14:01:11 +02:00 |
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sofstam
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1ba6a08135
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Seperate multiqc for filtlong
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2022-07-19 13:53:29 +02:00 |
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James Fellows Yates
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33a5402b25
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Add emitting porechop logs to multiqc and fix collection of others
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2022-07-19 13:50:39 +02:00 |
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sofstam
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3f5fa8cc7a
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Merge branch 'dev' into update_filtlong
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2022-07-19 13:50:28 +02:00 |
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James A. Fellows Yates
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6f269a8245
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Merge pull request #101 from nf-core/motus/merge
Add motus/merge and biom support
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2022-07-19 13:41:51 +02:00 |
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mjamy
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035b4b7a17
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Update the dev branch with the DIAMOND module update
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2022-07-15 16:28:07 +02:00 |
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sofstam
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5a2fd260fd
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Log file into multiqc channel
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2022-07-15 12:50:50 +02:00 |
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James Fellows Yates
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d83c747533
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Fix modules JSON
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2022-07-15 12:38:20 +02:00 |
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James A. Fellows Yates
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c215ed5607
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Merge branch 'dev' into motus/merge
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2022-07-15 10:52:42 +02:00 |
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James A. Fellows Yates
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cc3967a3fd
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Apply suggestions from code review
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2022-07-15 10:51:41 +02:00 |
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sofstam
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6b00360ff5
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Merge branch 'dev' into update_filtlong
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2022-07-15 10:05:43 +02:00 |
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