Added classpath variable for cfsan to env in nextflow.

.gitignore

@@ -9,6 +9,7 @@ log
 .nextflow*
 .nextflow/
 results/
+results2/
 work/
 
 

conf/singularity.config

@@ -35,4 +35,5 @@ env {
      TRIMMOMATIC_PATH = "/scif/apps/trimmomatic/Trimmomatic-0.38"
      LC_ALL="en_GB.utf-8"
      LANG="en_GB.utf-8"
+  	 CLASSPATH='/scif/apps/varscan/varscan-2.3.9/varscan-2.3.9.jar:/scif/apps/picard/bin/picard.jar:/scif/apps/gatk/gatk-3.8/GenomeAnalysisTK.jar'
 }

config.file

@@ -73,7 +73,7 @@ OUTPUT_DIR=/home/smonzon/Documents/desarrollo/bacterial_wgs_training/test/output
 	# AAAA_01=AAAA_01_R1.fastq.gz    AAAA_01_R2.fastq.gz
 	# BBBB_02=BBBB_02_R1.fastq.gz    BBBB_02_R2.fastq.gz
 
-SAMPLES=RA-L2073:RA-L2281:RA-L2327:RA-L2391:RA-L2450:RA-L2677:RA-L2701:RA-L2709:RA-L2782:RA-L2805:RA-L2978
+SAMPLES=RA-L2073:RA-L2281:RA-L2327:RA-L2391:RA-L2450:RA-L2677:RA-L2701:RA-L2782:RA-L2805:RA-L2978
 
 RA-L2073=RA-L2073_R1_paired.fastq.gz	RA-L2073_R2_paired.fastq.gz
 RA-L2281=RA-L2281_R1_paired.fastq.gz	RA-L2281_R1_paired.fastq.gz
@@ -82,7 +82,6 @@ RA-L2391=RA-L2391_R1_paired.fastq.gz	RA-L2391_R2_paired.fastq.gz
 RA-L2450=RA-L2450_R1_paired.fastq.gz	RA-L2450_R2_paired.fastq.gz
 RA-L2677=RA-L2677_R1_paired.fastq.gz	RA-L2677_R2_paired.fastq.gz
 RA-L2701=RA-L2701_R1_paired.fastq.gz	RA-L2701_R2_paired.fastq.gz
-RA-L2709=RA-L2709_R1_paired.fastq.gz	RA-L2709_R2_paired.fastq.gz
 RA-L2782=RA-L2782_R1_paired.fastq.gz	RA-L2782_R2_paired.fastq.gz
 RA-L2805=RA-L2805_R1_paired.fastq.gz	RA-L2805_R2_paired.fastq.gz
 RA-L2978=RA-L2978_R1_paired.fastq.gz	RA-L2978_R2_paired.fastq.gz

config2.file

@@ -19,15 +19,15 @@ SEQ_TYPE=paired
 
 TRIMMING=NO
 CHECK_REFERENCES=YES
-MAPPING=YES
-DUPLICATE_FILTER=YES
-VARIANT_CALLING=YES
+MAPPING=NO
+DUPLICATE_FILTER=NO
+VARIANT_CALLING=NO
 KMERFINDER=NO
 SRST2=NO
-CFSAN=NO
-VCF_TO_MSA=YES
+CFSAN=YES
+VCF_TO_MSA=NO
 RAXML=YES
-STATS=YES
+STATS=NO
 
 ############################################# System variables #######################################################
 
@@ -73,7 +73,7 @@ OUTPUT_DIR=/home/smonzon/Documents/desarrollo/bacterial_wgs_training/results/wgs
 	# AAAA_01=AAAA_01_R1.fastq.gz    AAAA_01_R2.fastq.gz
 	# BBBB_02=BBBB_02_R1.fastq.gz    BBBB_02_R2.fastq.gz
 
-SAMPLES=RA-L2073:RA-L2281:RA-L2327:RA-L2391:RA-L2450:RA-L2677:RA-L2701:RA-L2709:RA-L2782:RA-L2805:RA-L2978
+SAMPLES=RA-L2073:RA-L2281:RA-L2327:RA-L2391:RA-L2450:RA-L2677:RA-L2701:RA-L2782:RA-L2805:RA-L2978
 
 RA-L2073=RA-L2073_R1_paired.fastq.gz	RA-L2073_R2_paired.fastq.gz
 RA-L2281=RA-L2281_R1_paired.fastq.gz	RA-L2281_R1_paired.fastq.gz
@@ -82,7 +82,6 @@ RA-L2391=RA-L2391_R1_paired.fastq.gz	RA-L2391_R2_paired.fastq.gz
 RA-L2450=RA-L2450_R1_paired.fastq.gz	RA-L2450_R2_paired.fastq.gz
 RA-L2677=RA-L2677_R1_paired.fastq.gz	RA-L2677_R2_paired.fastq.gz
 RA-L2701=RA-L2701_R1_paired.fastq.gz	RA-L2701_R2_paired.fastq.gz
-RA-L2709=RA-L2709_R1_paired.fastq.gz	RA-L2709_R2_paired.fastq.gz
 RA-L2782=RA-L2782_R1_paired.fastq.gz	RA-L2782_R2_paired.fastq.gz
 RA-L2805=RA-L2805_R1_paired.fastq.gz	RA-L2805_R2_paired.fastq.gz
 RA-L2978=RA-L2978_R1_paired.fastq.gz	RA-L2978_R2_paired.fastq.gz