From eb2c7b8e6a9226cbd82553cdad17a60aed831d11 Mon Sep 17 00:00:00 2001
From: Stephen Newhouse <stephen.j.newhouse@gmail.com>
Date: Tue, 8 Sep 2015 13:17:36 +0100
Subject: [PATCH] dev updates Tue  8 Sep 2015 13:17:36 BST

---
 bin/ngseasy_trimmomatic | 41 ++++++++++-------------------------------
 1 file changed, 10 insertions(+), 31 deletions(-)

diff --git a/bin/ngseasy_trimmomatic b/bin/ngseasy_trimmomatic
index 71f7986..b3cfd4a 100755
--- a/bin/ngseasy_trimmomatic
+++ b/bin/ngseasy_trimmomatic
@@ -409,7 +409,6 @@ fi
 ########################################################################################################
 # adapter_fa : check of this is in palce and exit if not
 ########################################################################################################
-
 if [[ ${GENOMEBUILD} == "b37" ]]; then
     adapter_fa="/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_b37/contaminant_list.fa"
 elif [[ ${GENOMEBUILD} == "hg19" ]]; then
@@ -419,7 +418,6 @@ elif [[ "${GENOMEBUILD}" == "hs37d5" ]]; then
 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}
 
 ########################################################################################################
@@ -464,19 +462,17 @@ if [ -s "${SOUT}/fastq/${SAMPLE_ID}.${NGS_TYPE}.${DNA_PREP_LIBRARY_ID}.${TRIM}_1
 then
 	logger_ngseasy "[${NGSEASY_STEP}]:PE Trimmed Data already exists...skipping [${NGSEASY_STEP}]" ${LOGFILE}
 
+########################################################################################################
+## atrim
 elif [[ "$TRIM" == "atrim" ]]; then
 	logger_ngseasy "[${NGSEASY_STEP}]:Trimmomatic not run yet" ${LOGFILE}
 
 ########################################################################################################
 ## run compbio/ngseasy-trimmomatic
-#
+########################################################################################################
 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}/ngseasy_resources"
-
 ## run trimmomatic
 #
 logger_ngseasy "[${NGSEASY_STEP}]:[cmd]: ILLUMINACLIP:${adapter_fa}:2:30:10:5:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 AVGQUAL:2 MINLEN:75 " ${LOGFILE}
@@ -502,8 +498,9 @@ logger_ngseasy "[${NGSEASY_STEP}]:[cmd]: ILLUMINACLIP:${adapter_fa}:2:30:10:5:tr
 
 logger_ngseasy "[${NGSEASY_STEP}]:FastQC post Trimmomatic" ${LOGFILE}
 
+########################################################################################################
 ##  compbio/ngseasy-fastqc
-#
+########################################################################################################
 	${DOCKER_RUN} \
 	--rm=true \
 	-v ${PROJECT_DIR}:/home/pipeman/ngs_projects \
@@ -522,34 +519,15 @@ logger_ngseasy "[${NGSEASY_STEP}]:FastQC post Trimmomatic" ${LOGFILE}
 ########################################################################################################
 ## Just QC FASTQ NO ADAPTOR TRIM
 # btrim is basic qc-trim
-#
+########################################################################################################
 elif [[ "$TRIM" == "btrim" ]]; then
 
 logger_ngseasy "[${NGSEASY_STEP}]:START qc of raw fastq files" ${LOGFILE}
 logger_ngseasy "[${NGSEASY_STEP}]:TRIM set to [$TRIM] - basic trim. Just read quality trimming. No adaptor trimming" ${LOGFILE}
 
-#if [[ ! -s ${SOUT}/fastq/${FQ1}.art_filt.gz  ]] && [[ ! -s ${SOUT}/fastq/${FQ2}.art_filt.gz ]]; then
-## make parallel cmd
-#
-#echo -e "
-#zcat ${SOUTDocker}/fastq/${FQ1} | fastx_artifacts_filter -Q33 -i - -z -o ${SOUTDocker}/fastq/${FQ1}.art_filt.gz
-#zcat ${SOUTDocker}/fastq/${FQ2} | fastx_artifacts_filter -Q33 -i - -z -o ${SOUTDocker}/fastq/${FQ2}.art_filt.gz
-#" > ${SOUT}/parallel_fastx.cmd
-#
-## run fastx_artifacts_filter
-#
-#logger_ngseasy "[${NGSEASY_STEP}]:[cmd]: fastx_artifacts_filter. Removing Homopolymer reads" ${LOGFILE}
-#
-#	${DOCKER_RUN} \
-#	--rm=true \
-#	-v ${PROJECT_DIR}:/home/pipeman/ngs_projects \
-#	--name fastx_artifacts_filter_${BAM_PREFIX} \
-#	-t compbio/ngseasy-trimmomatic:${NGSEASYVERSION} /bin/bash -c "cat ${SOUTDocker}/parallel_fastx.cmd | parallel -j 2 --no-notice"
-#fi
-
-
+########################################################################################################
 ## run trimmomatic
-#
+########################################################################################################
 	${DOCKER_RUN} \
 	--rm=true \
 	-v ${PROJECT_DIR}:/home/pipeman/ngs_projects \
@@ -569,8 +547,9 @@ logger_ngseasy "[${NGSEASY_STEP}]:TRIM set to [$TRIM] - basic trim. Just read qu
 
 logger_ngseasy "[${NGSEASY_STEP}]:START FastQC post Trimmomatic" ${LOGFILE}
 
+########################################################################################################
 ##  compbio/ngseasy-fastqc
-#
+########################################################################################################
 	${DOCKER_RUN} \
 	--rm=true \
 	-v ${PROJECT_DIR}:/home/pipeman/ngs_projects \