From b480bb478ec500b7a2c6f89a5cdea6d8fb085c33 Mon Sep 17 00:00:00 2001
From: taranewman <tara.newman98@gmail.com>
Date: Wed, 20 Nov 2024 11:31:13 -0800
Subject: [PATCH 1/4] remove testing num isolates within snippy core module

---
 main.nf                | 9 +++------
 modules/gubbins.nf     | 3 ---
 modules/snippy_core.nf | 9 +--------
 3 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/main.nf b/main.nf
index ee30ed6..744c847 100644
--- a/main.nf
+++ b/main.nf
@@ -34,12 +34,9 @@ workflow {
 
   
   if (!params.skip_gubbins) {
-    gubbins(snippy_core.out.clean_full_alignment, snippy_core.out.run_gubbins)
-    if (snippy_core.out.run_gubbins == "true") {
-      ch_alignment = gubbins.out.filtered_polymorphic_sites
-    } else {
-      ch_alignment = snippy_core.out.clean_full_alignment
-    }
+    gubbins(snippy_core.out.clean_full_alignment)
+    ch_alignment = gubbins.out.filtered_polymorphic_sites
+
   } else {
     ch_alignment = snippy_core.out.clean_full_alignment
   }
diff --git a/modules/gubbins.nf b/modules/gubbins.nf
index b1de688..5f04078 100644
--- a/modules/gubbins.nf
+++ b/modules/gubbins.nf
@@ -6,15 +6,12 @@ process gubbins {
 
   input:
   path(alignment)
-  val(run_gubbins)
 
   output:
   path('gubbins.filtered_polymorphic_sites.fasta'), emit: filtered_polymorphic_sites
   path('gubbins.recombination_predictions.gff'),    emit: recombination_predictions_gff
   path('gubbins.per_branch_statistics.tsv'),        emit: per_branch_statistics
 
-  when:
-  run_gubbins == "true"
 
   script:
   """
diff --git a/modules/snippy_core.nf b/modules/snippy_core.nf
index b521c6d..1edb064 100644
--- a/modules/snippy_core.nf
+++ b/modules/snippy_core.nf
@@ -12,10 +12,10 @@ process snippy_core {
     path('core.tsv'), emit: core_stats
     path('core.full.aln'), emit: full_alignment
     path('clean.full.aln'), emit: clean_full_alignment
-    val('run_gubbins'), emit: run_gubbins
 
 
     script:
+    
     """
     snippy-core \
       --ref ${ref} \
@@ -26,13 +26,6 @@ process snippy_core {
 
     add_percent_used.py core.txt > core.tsv
 
-    num_isolates=\$(echo "\$snippy_dirs" | tr -s ' ' | wc -w)
-    if [ "\$num_isolates" -ge 3 ]; then
-        run_gubbins='true'
-    else
-        run_gubbins='false'
-    fi
-    
     """
 }
 

From 809fdaeba07c0908916856cfebedb2f7869c8248 Mon Sep 17 00:00:00 2001
From: taranewman <tara.newman98@gmail.com>
Date: Wed, 20 Nov 2024 11:33:50 -0800
Subject: [PATCH 2/4] correct pipeline name in readme

---
 README.md              | 2 +-
 modules/snippy_core.nf | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 2ad6f5f..c7c5eb8 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ Note: the process WITHOUT gubbins occurs if --skip_gubbins is true, or if there
 ## Usage
 
 ```
-nextflow run BCCDC-PHL/snippy-phylogenomics-nf \
+nextflow run BCCDC-PHL/snippy-core-phylogenomics \
   --snippy_dirs </path/to/snippy_output_dirs> \
   --ref ref.fa \
   [--mask mask.bed] \
diff --git a/modules/snippy_core.nf b/modules/snippy_core.nf
index 1edb064..9408ccb 100644
--- a/modules/snippy_core.nf
+++ b/modules/snippy_core.nf
@@ -15,7 +15,6 @@ process snippy_core {
 
 
     script:
-    
     """
     snippy-core \
       --ref ${ref} \

From e2f3d15ac97eb5e9a8dec5a16ff1573f7f9d2896 Mon Sep 17 00:00:00 2001
From: taranewman <tara.newman98@gmail.com>
Date: Wed, 20 Nov 2024 11:34:50 -0800
Subject: [PATCH 3/4] remove defaults

---
 environments/environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environments/environment.yml b/environments/environment.yml
index 8b206d6..6c72e7d 100644
--- a/environments/environment.yml
+++ b/environments/environment.yml
@@ -2,7 +2,6 @@ name: snippy-phylogenomics
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python
   - snippy=4.6.0

From 1b7d5c149240f9180e07392ba386473c62b27a8c Mon Sep 17 00:00:00 2001
From: taranewman <tara.newman98@gmail.com>
Date: Wed, 20 Nov 2024 12:55:44 -0800
Subject: [PATCH 4/4] restore defaults due to conda issue

---
 environments/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environments/environment.yml b/environments/environment.yml
index 6c72e7d..8b206d6 100644
--- a/environments/environment.yml
+++ b/environments/environment.yml
@@ -2,6 +2,7 @@ name: snippy-phylogenomics
 channels:
   - conda-forge
   - bioconda
+  - defaults
 dependencies:
   - python
   - snippy=4.6.0