From ffcafe47a96e594d59cd2027e74763374ef07c23 Mon Sep 17 00:00:00 2001 From: saramonzon Date: Fri, 26 Oct 2018 10:33:31 +0200 Subject: [PATCH] Added classpath variable for cfsan to env in nextflow. --- .gitignore | 1 + conf/singularity.config | 1 + config.file | 3 +-- config2.file | 15 +++++++-------- scif_app_recipes | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.gitignore b/.gitignore index 2f13703..14dec95 100644 --- a/.gitignore +++ b/.gitignore @@ -9,6 +9,7 @@ log .nextflow* .nextflow/ results/ +results2/ work/ diff --git a/conf/singularity.config b/conf/singularity.config index 60b00ea..962948b 100644 --- a/conf/singularity.config +++ b/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' } diff --git a/config.file b/config.file index b79cab2..1821782 100644 --- a/config.file +++ b/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 diff --git a/config2.file b/config2.file index 3c6d690..b7bad3a 100644 --- a/config2.file +++ b/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 diff --git a/scif_app_recipes b/scif_app_recipes index a4edefa..e9a39f3 160000 --- a/scif_app_recipes +++ b/scif_app_recipes @@ -1 +1 @@ -Subproject commit a4edefaf8521d278f13c239b3349ade3bace9a77 +Subproject commit e9a39f3f3b3903c6bc7589937d1af43e386f671d