diff --git a/bin/ngseasy_trimmomatic b/bin/ngseasy_trimmomatic index b207573..71f7986 100755 --- a/bin/ngseasy_trimmomatic +++ b/bin/ngseasy_trimmomatic @@ -409,7 +409,17 @@ fi ######################################################################################################## # adapter_fa : check of this is in palce and exit if not ######################################################################################################## -adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_b37/contaminant_list.fa" + +if [[ ${GENOMEBUILD} == "b37" ]]; then + adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_b37/contaminant_list.fa" +elif [[ ${GENOMEBUILD} == "hg19" ]]; then + adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hg19/contaminant_list.fa" +elif [[ "${GENOMEBUILD}" == "hs37d5" ]]; then + adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hs37d5/contaminant_list.fa" +elif [[ "${GENOMEBUILD}" == "hs38DH" ]]; then + adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hs38DH/contaminant_list.fa" +fi + logger_ngseasy "[${NGSEASY_STEP}]:setting adaptor list docker dir [$adapter_fa]" ${LOGFILE} ######################################################################################################## @@ -464,8 +474,8 @@ logger_ngseasy "[${NGSEASY_STEP}]:START qc of raw fastq files" ${LOGFILE} logger_ngseasy "[${NGSEASY_STEP}]:TRIM set to [$TRIM] - adaptor trim. Adaptor and read quality trimming" ${LOGFILE} ## get ngs_resource mapping -myresources=`dirname ${PROJECT_DIR}` -NGSResources="${myresources}/ngs_resources" +##myresources=`dirname ${PROJECT_DIR}` +##NGSResources="${myresources}/ngseasy_resources" ## run trimmomatic #