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)