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comparison updating-to-pipeline-1.3-DADA2.txt @ 4:86a12d75ebe4 draft default tip

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8
author pjbriggs
date Fri, 20 Dec 2019 06:59:49 -0500
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3:3ab198df8f3f 4:86a12d75ebe4
1 Notes on updating Galaxy tool to pipeline 1.3 (DADA2)
2 =====================================================
3
4 Where stuff is:
5
6 * projects/Amplicon_analysis-galaxy: git repo for Galaxy tool (these
7 developments are in the 'update-to-Amplicon_analysis_pipeline-1.3'
8 branch, PR #50:
9 https://github.com/pjbriggs/Amplicon_analysis-galaxy/pull/50)
10
11 * scratchpad/test_Amplicon_analysis_pipeline_DADA2: directory for
12 running/testing the updates
13
14 So far:
15
16 * Updated the installer for pipeline version 1.3.2
17
18 * Have been trying to run the pipeline manually outside of Galaxy
19 on popov & CSF3:
20 -- DADA2 works on popov (can't remember if it works on CSF3)
21 -- Vsearch pipeline fails on popov and CSF3 (but errors are
22 different)
23
24 * Mauro is looking at fixing the errors while I carry on trying
25 to update the Galaxy tool
26
27 Random notes from my notebook:
28
29 p44:
30
31 * DADA2 uses NSLOTS environment variable from the local environment
32 (so can get number of cores on cluster; if NSLOTS not set then
33 gets number of cores on local machine)
34
35 * DADA2 has new outputs:
36 -- DADA2_OTU_tables/Error_rate_plots/ <-- need to capture all
37 PDFs from this folder
38
39 pp78-79:
40
41 * Galaxy wrapper could check that 'Run' column is in supplied
42 metatable file (if it's not present then pipeline will fail
43 now)
44
45 * DADA2 has its own reference database
46
47 * DADA2 produces same outputs as Vsearch (with name changed from
48 "Vsearch_*" to "DADA2_*", plus extras:
49 -- Vsearch_OTUs.tre -> otus.tre
50 -- Vsearch_multiplexed_linearised_dereplicated_mc2_repset_nonchimeras_OTUS.fasta -> seqs.fa
51 -- There might be issues with the heatmap
52
53 p83: notes on progress...
54
55 p95:
56
57 * Confirms heatmap is now e.g. RESULTS/Vsearch_silva/Heatmap.pdf
58 (instead of HTML output)