AMR++ v2.0.2

meglab-metagenomics · May 21, 2020 · c610213 · c610213
1 parent c3dad18
commit c610213
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Showing 6 changed files with 13 additions and 8 deletions.
diff --git a/README.md b/README.md
@@ -12,6 +12,10 @@ We identified issues in running RGI with the full AMR++ pipeline thanks to githu
   * To run the AMR++ pipeline with RGI, you'll have to download the CARD database locally and specify it's location using the "--card_db" flag like this:
 
 ```
+# If you want to include RGI in your analysis, first download CARD with this command:
+wget -q -O card-data.tar.bz2 https://card.mcmaster.ca/latest/data && tar xfvj card-data.tar.bz2
+
+# Run the AMR++ pipeline with the "--card_db" flag
 nextflow run main_AmrPlusPlus_v2_withRGI.nf -profile singularity --card_db /path/to/card.json --reads '/path/to/reads/*R{1,2}_001.R1.fastq.gz' --output AMR++_results -w work_dir
 ```
 

diff --git a/config/.singularity.config.swp b/config/.singularity.config.swp
diff --git a/config/singularity.config b/config/singularity.config
@@ -29,6 +29,9 @@ process {
   process.container = 'shub://meglab-metagenomics/amrplusplus_v2'
   maxForks = 10                 // The maximum number of forks a single process is allowed to spawn
   withName:RunRGI {
-    process.container 'shub://meglab-metagenomics/amrplusplus_v2:rgi'
+    container = 'shub://meglab-metagenomics/amrplusplus_v2:rgi'
+  }
+  withName:RunDedupRGI {
+    container = 'shub://meglab-metagenomics/amrplusplus_v2:rgi'
   }
 }
diff --git a/config/singularity_slurm.config b/config/singularity_slurm.config
@@ -22,9 +22,6 @@ env {
     KRAKEN2 = "kraken2"
     RGI = "/opt/conda/envs/PI_env/bin/rgi"
     DIAMOND = "diamond"
-    BBMAP_JAVA= "/usr/local/bbmap/jni/"
-    BBMAP_current = "/usr/local/bbmap/current/"
-    CLUMPIFY = "-ea -cp /usr/local/bbmap/current/ clump.Clumpify"
 }
 
 
@@ -164,7 +161,7 @@ process {
   }
   withName:RunRGI {
       process.qos='normal'
-      process.container 'shub://EnriqueDoster/bioinformatic-nextflow-pipelines:rgi'
+      container = 'shub://EnriqueDoster/bioinformatic-nextflow-pipelines:rgi'
       clusterOptions='--job-name=RunRGI%j --qos=normal --time=23:59:00'
   }
   withName:SNPconfirmation {
@@ -185,7 +182,7 @@ process {
   }
   withName:RunDedupRGI {
       process.qos='normal'
-      process.container 'shub://EnriqueDoster/bioinformatic-nextflow-pipelines:rgi'
+      container = 'shub://EnriqueDoster/bioinformatic-nextflow-pipelines:rgi'
       clusterOptions='--job-name=RunDedupRGI --qos=normal --time=23:59:00'
   }
   withName:DedupSNPconfirmation {

diff --git a/containers/Singularity.RGI b/containers/Singularity.RGI
@@ -40,8 +40,8 @@ From: debian:jessie-slim
 
      # This downloads the latest CARD database and attempts to load it for RGI
      # Doesn't seem to work due to the github [RGI issue #60](https://github.com/arpcard/rgi/issues/60)
-     wget -q -O card-data.tar.bz2 https://card.mcmaster.ca/latest/data && tar xfvj card-data.tar.bz2 
-     /usr/local/envs/AmrPlusPlus_env/bin/rgi load -i card.json
+     #wget -q -O card-data.tar.bz2 https://card.mcmaster.ca/latest/data && tar xfvj card-data.tar.bz2 
+     #/usr/local/envs/AmrPlusPlus_env/bin/rgi load -i card.json
 
 %test
 

diff --git a/main_AmrPlusPlus_v2_withRGI_Kraken.nf b/main_AmrPlusPlus_v2_withRGI_Kraken.nf
@@ -32,6 +32,7 @@ if(params.kraken_db) {
     kraken_db = file(params.kraken_db)
 }
 
+card_db = file(params.card_db)
 
 threads = params.threads
-Original file line number
+Diff line change
@@ Expand Up / @@ -32,6 +32,7 @@ if(params.kraken_db) { @@
         kraken_db = file(params.kraken_db)
     }
+    card_db = file(params.card_db)
     threads = params.threads
@@ Expand Down @@