reduce testing assembly, disable branch support default

ktmeaton · Jun 19, 2020 · 3cebf05 · 3cebf05
1 parent c3e5426
commit 3cebf05
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Showing 4 changed files with 16 additions and 9 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,8 +16,8 @@ and this project "attempts" to adhere to [Semantic Versioning](http://semver.org
 - Make the snippy multi filter locus splitting be generic (not plague specific)
 - Deal with nextstrain augur not working with phylogeny with branch support values
 - Breakup snippy step in pipeline to snippy - snp stats - snpeff
-- Add outgroup 2 x Y. pseudotuberculosis
-- Move config files to config directory
+- Allow input of own contig files (param)
+- Allow input of own fastq files (tsv concat)
 
 ## [v0.1.4] - 2020-06-18 - SRA and nf-core/eager
 

diff --git a/README.md b/README.md
@@ -74,7 +74,7 @@ conda install -n nf-core-eager-2.2.0dev -c anaconda graphviz
 ```bash
 conda activate plague-phylogeography-0.1.4dev
 nextflow run ktmeaton/plague-phylogeography \
-  --max_datasets_assembly 4 \
+  --max_datasets_assembly 2 \
   --max_datasets_sra 1 \
   --skip_outgroup_download \
   --iqtree_runs 1 \

diff --git a/main.nf b/main.nf
@@ -1188,19 +1188,26 @@ process iqtree{
     OUTGROUP=${params.iqtree_outgroup}
   fi
 
+  # Setup the branch support param
+  if [[ ${params.skip_outgroup_download} == "true"  ]]; then
+    BRANCH_SUPPORT="--bnni --alrt ${params.iqtree_alrt} --ufboot ${params.iqtree_ufboot}";
+    SUFFIX="_bootstrap";
+  else
+    BRANCH_SUPPORT="";
+    SUFFIX="";
+  fi
+
   # A thorough tree search for model selection can be done with -m MF -mtree
   iqtree \
     -s ${snippy_core_filter_aln} \
     -m MFP \
     -nt AUTO \
     -o \$OUTGROUP \
     -seed \$RANDOM \
-    --bnni \
-    --alrt ${params.iqtree_alrt} \
-    --ufboot ${params.iqtree_ufboot} \
+    \${BRANCH_SUPPORT} \
     --runs ${params.iqtree_runs} \
-    -pre iqtree.core-filter${params.snippy_multi_missing_data_text}_bootstrap \
-    2>&1 | tee iqtree.core-filter${params.snippy_multi_missing_data_text}_bootstrap.output
+    -pre iqtree.core-filter${params.snippy_multi_missing_data_text}\${SUFFIX} \
+    2>&1 | tee iqtree.core-filter${params.snippy_multi_missing_data_text}\${SUFFIX}.output
   """
 }
 

diff --git a/nextflow.config b/nextflow.config
@@ -127,9 +127,9 @@ params{
   iqtree_outgroup = "Reference"
   // Could be manually specified, and/or multi
   //iqtree_outgroup = "Sample1,Sample2"
+  iqtree_branch_support = false
   iqtree_alrt = 1000
   iqtree_ufboot = 1000
-  iqtree_runs = 10
 
   // SQLite query
   sqlite_select_command_asm = "\'SELECT AssemblyFTPGenbank FROM Master WHERE BioSampleComment LIKE \"%KEEP%\"\'"