Merge pull request #14 from hariszaf/develop

ITS added as in the new architecture
hariszaf · Jun 5, 2021 · 4ec148a · 4ec148a
2 parents 7ba6d6d + 2db3e5b
commit 4ec148a
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Showing 5 changed files with 36 additions and 17 deletions.
diff --git a/Singularity b/Singularity
@@ -11,8 +11,8 @@ echo "export WORKDIR=$WORKDIR" >> $SINGULARITY_ENVIRONMENT
 mkdir -p $WORKDIR
 
 # Exports needed
-echo "export PATH=/usr/lib/jvm/java-8-openjdk-amd64/bin:/usr/lib/jvm/java-11-openjdk-amd64/bin:/opt/java/openjdk/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/tools/BDS/.bds" >> $SINGULARITY_ENVIRONMENT 
-echo "export PATH=$PATH:/bin/gzip" >> ~/.bashrc 
+echo "export PATH=/usr/lib/jvm/java-8-openjdk-amd64/bin:/usr/lib/jvm/java-11-openjdk-amd64/bin:/opt/java/openjdk/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/tools/BDS/.bds:/bin/gzip" >> $SINGULARITY_ENVIRONMENT 
+#echo "export PATH=$PATH:/bin/gzip" >> ~/.bashrc 
 
 
 # Set basecommnad; run PEMA analysis

diff --git a/pema_docker_image/modules/clustering.bds b/pema_docker_image/modules/clustering.bds
@@ -85,7 +85,7 @@ string clusteringVsearch(string{} params, string{} globalVars) {
 
 }
 
-
+# Function to get ASVs using the Swarm v2 algorithm
 string clusteringSwarm(string{} params, string{} globalVars) {
 
 
@@ -161,7 +161,7 @@ string clusteringSwarm(string{} params, string{} globalVars) {
 
       wait
 
-   } else if ( params{'classifierAlgo'} == 'CREST' && params{'gene'} != 'gene_COI' ) {
+   } else if ( params{'classifierAlgo'} == 'CREST' && params{'gene'} == 'gene_COI' ) {
 
       println('You have selected CREST classifier and your marker gene is COI. Pema does not support this combination.')
 
@@ -176,9 +176,6 @@ string clusteringSwarm(string{} params, string{} globalVars) {
 }
 
 
-
-
-
 string swarmMinValues(string{} params, string{} globalVars) {
 
    int d_param = params{'d'}.parseInt()
@@ -236,7 +233,6 @@ string swarmMinValues(string{} params, string{} globalVars) {
 
 }  
 
-
 # In this case, chimera removal goes before the ASVs inference
 string swarmMaxValues(string{} params, string{} globalVars){
 
@@ -275,7 +271,11 @@ string swarmMaxValues(string{} params, string{} globalVars){
 }
 
 
-
+# Function to get OTUs using the Bayesian algorithm CROP; this will take significant more time
+string clusteringCrop(string{} params, string{} globalVars){
+   println('this is crop')
+   return 'ok'
+}
 
 
 

diff --git a/pema_docker_image/modules/taxAssignment.bds b/pema_docker_image/modules/taxAssignment.bds
@@ -72,9 +72,32 @@ string crestAssign(string{} params, string{} globalVars) {
          wait
 
 
-      } else {
+      } else if (params{'gene'}  == 'gene_ITS') {
+
+         globalVars{'assignmentPath'}.chdir()
+
+         task $globalVars{'path'}/tools/ncbi-blast-2.8.1+/bin/blastn -task megablast \
+            -query all_sequences_grouped.fa \
+            -db $globalVars{'path'}/tools/CREST/LCAClassifier/parts/flatdb/unite/unite.fasta \
+            -num_alignments 100 -outfmt 5 \
+            -out unite_$params{'taxonomyFolderName'}.xml \
+            -num_threads $params{'vsearchThreads'}
 
-         println("one step at a time dude. this is for the ITS case.")
+         wait
+
+         task $globalVars{'path'}/tools/CREST/LCAClassifier/bin/classify \
+            -c $globalVars{'path'}/tools/CREST/LCAClassifier/parts/etc/lcaclassifier.conf \
+            -d unite \
+            -t allTab_$params{'taxonomyFolderName'}.tsv \
+            -o $params{'taxonomyFolderName'} unite_$params{'taxonomyFolderName'}.xml
+
+         wait
+
+         task {
+            sys mv $params{'taxonomyFolderName'}/allTab_$params{'taxonomyFolderName'}.tsv $params{'taxonomyFolderName'}/finalTable.tsv
+            sys sed -i 's/classification/Classification/g' $params{'taxonomyFolderName'}/finalTable.tsv
+         }
+         wait
       }
 
    } else {

diff --git a/pema_docker_image/pema_latest.bds b/pema_docker_image/pema_latest.bds
@@ -40,7 +40,7 @@ wait
 ###############################################################
 
 qualityControl(paramsFirstAssignment, globalVars)
-
+wait
 ################################################################
 #                   2. Trimming                                #
 ################################################################

diff --git a/pema_docker_image/scripts/cutadaptITS.R b/pema_docker_image/scripts/cutadaptITS.R
@@ -72,11 +72,7 @@ for (base in reverse_split) {
 ##########################################################################################
 
 # (let us hope) singularity version
-<<<<<<< HEAD
 cutadapt <- "/usr/bin/cutadapt3"
-=======
-cutadapt <- "/usr/bin/cutadapt"
->>>>>>> local_ref_db
 
 
 system2(cutadapt, args = "--version") # Run shell commands from R
@@ -119,7 +115,7 @@ R2.flags <- paste("-G", REV, "-A", FWD.RC)
 
 # Run Cutadapt
 for(i in seq_along(fnFs)) {
-  system2(cutadapt, args = c(R1.flags, R2.flags, "-n", 2, "-j", 0,     # -n 2 required to remove FWD and REV from reads
+  system2(cutadapt, args = c(R1.flags, R2.flags, "-n", 2,     # -n 2 required to remove FWD and REV from reads
                              "-o", fnFs.cut[i], "-p", fnRs.cut[i],     # output files
                              fnFs[i], fnRs[i]))                        # input files
 }