--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/updating-to-pipeline-1.3-DADA2.txt	Fri Dec 20 06:59:49 2019 -0500
@@ -0,0 +1,58 @@
+Notes on updating Galaxy tool to pipeline 1.3 (DADA2)
+=====================================================
+
+Where stuff is:
+
+* projects/Amplicon_analysis-galaxy: git repo for Galaxy tool (these
+  developments are in the 'update-to-Amplicon_analysis_pipeline-1.3'
+  branch, PR #50:
+  https://github.com/pjbriggs/Amplicon_analysis-galaxy/pull/50)
+
+* scratchpad/test_Amplicon_analysis_pipeline_DADA2: directory for
+  running/testing the updates
+
+So far:
+
+* Updated the installer for pipeline version 1.3.2
+
+* Have been trying to run the pipeline manually outside of Galaxy
+  on popov & CSF3:
+  -- DADA2 works on popov (can't remember if it works on CSF3)
+  -- Vsearch pipeline fails on popov and CSF3 (but errors are
+     different)
+
+* Mauro is looking at fixing the errors while I carry on trying
+  to update the Galaxy tool
+
+Random notes from my notebook:
+
+p44:
+
+* DADA2 uses NSLOTS environment variable from the local environment
+  (so can get number of cores on cluster; if NSLOTS not set then
+  gets number of cores on local machine)
+
+* DADA2 has new outputs:
+  -- DADA2_OTU_tables/Error_rate_plots/ <-- need to capture all
+     PDFs from this folder
+
+pp78-79:
+
+* Galaxy wrapper could check that 'Run' column is in supplied
+  metatable file (if it's not present then pipeline will fail
+  now)
+
+* DADA2 has its own reference database
+
+* DADA2 produces same outputs as Vsearch (with name changed from
+  "Vsearch_*" to "DADA2_*", plus extras:
+  -- Vsearch_OTUs.tre -> otus.tre
+  -- Vsearch_multiplexed_linearised_dereplicated_mc2_repset_nonchimeras_OTUS.fasta -> seqs.fa
+  -- There might be issues with the heatmap
+
+p83: notes on progress...
+
+p95:
+
+* Confirms heatmap is now e.g. RESULTS/Vsearch_silva/Heatmap.pdf
+  (instead of HTML output)