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dev updates Tue 8 Sep 2015 13:17:36 BST
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snewhouse committed Sep 8, 2015
1 parent 57c29fb commit eb2c7b8
Showing 1 changed file with 10 additions and 31 deletions.
41 changes: 10 additions & 31 deletions bin/ngseasy_trimmomatic
Original file line number Diff line number Diff line change
Expand Up @@ -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 [[ ${GENOMEBUILD} == "hg19" ]]; then
Expand All @@ -419,7 +418,6 @@ elif [[ "${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}

########################################################################################################
Expand Down Expand Up @@ -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 " ${LOGFILE}
Expand All @@ -502,8 +498,9 @@ logger_ngseasy "[${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 ${PROJECT_DIR}:/home/pipeman/ngs_projects \
Expand All @@ -522,34 +519,15 @@ logger_ngseasy "[${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 ${PROJECT_DIR}:/home/pipeman/ngs_projects \
Expand All @@ -569,8 +547,9 @@ logger_ngseasy "[${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 \
Expand Down

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