From 76d6d7310d205ee26669b7083103f06aee66d1a1 Mon Sep 17 00:00:00 2001
From: fmalmeida <felipemarques89@gmail.com>
Date: Wed, 12 Jan 2022 13:42:46 +0100
Subject: [PATCH] Fixed how quast is executed accross different profiles
 conda/docker/singularity

---
 modules/QualityAssessment/quast.nf | 20 +++++++++++++++++++-
 nextflow.config                    | 29 ++++++++++++++++-------------
 2 files changed, 35 insertions(+), 14 deletions(-)

diff --git a/modules/QualityAssessment/quast.nf b/modules/QualityAssessment/quast.nf
index 59210d82..85d80564 100644
--- a/modules/QualityAssessment/quast.nf
+++ b/modules/QualityAssessment/quast.nf
@@ -14,9 +14,27 @@ process quast {
   single_param = !(single =~ /input.?/) ? "--single ${single}" : ""
   lreads_param = !(lreads =~ /input.?/) ? "--${lr_type} ${lreads}" : ""
 
+  if (params.selected_profile == "docker" || params.selected_profile == "conda")
+  """
+  # run quast
+  quast.py \\
+      -o ${assembler} \\
+      -t ${params.threads} \\
+      ${lreads_param} \\
+      ${paired_param} \\
+      ${single_param} \\
+      --conserved-genes-finding \\
+      --rna-finding \\
+      --min-contig 100 \\
+      ${params.quast_additional_parameters} \\
+      ${contigs}
+  """
+
+  else if (params.selected_profile == "singularity")
   """
   # fix busco usage in singularity
-  cp -R $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/busco ~/.quast
+  mkdir -p ~/.quast/busco
+  cp -R /opt/conda/envs/mpgap-*/lib/python3.6/site-packages/quast_libs/busco ~/.quast
 
   # run quast
   quast.py \\
diff --git a/nextflow.config b/nextflow.config
index fcca1766..e79fad6d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -193,27 +193,30 @@ profiles {
 
   // conda profile
   conda {
-    singularity.enabled   = false
-    docker.enabled        = false
-    process.conda         = "$CONDA_PREFIX/envs/mpgap-3.1"
+    params.selected_profile = "conda"
+    singularity.enabled     = false
+    docker.enabled          = false
+    process.conda           = "$CONDA_PREFIX/envs/mpgap-3.1"
   }
 
   // docker profile
   docker      {
-    singularity.enabled = false
-    docker.enabled      = true
-    docker.runOptions   = '-u \$(id -u):\$(id -g)'
-    fixOwnership        = true
-    process.container   = "fmalmeida/mpgap:v3.1"
+    params.selected_profile = "docker"
+    singularity.enabled     = false
+    docker.enabled          = true
+    docker.runOptions       = '-u \$(id -u):\$(id -g)'
+    fixOwnership            = true
+    process.container       = "fmalmeida/mpgap:v3.1"
   }
 
   // singularity profile
   singularity {
-    docker.enabled         = false
-    singularity.enabled    = true
-    singularity.autoMounts = true
-    process.container      = "docker://fmalmeida/mpgap:v3.1"
-    singularity.autoMounts = true
+    params.selected_profile = "singularity"
+    docker.enabled          = false
+    singularity.enabled     = true
+    singularity.autoMounts  = true
+    process.container       = "docker://fmalmeida/mpgap:v3.1"
+    singularity.autoMounts  = true
   }
 
 }