Can use cutadapt or fastx_clipper to trim adapter.

PRO-seq/PRO-seq_trim_and_dedup.sh

 #!/usr/bin/env bash
-# Usage: PRO-seq_trim_and_dedup.sh <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <cutadapt log> <nb_raw> <nb_adapt> <nb_adapt_deduped> <nb_noadapt> <nb_noadapt_deduped>
+# Usage: PRO-seq_trim_and_dedup.sh <trimmer> <raw fastq> <ADAPTER> <nb 5'> <nb 3'> <trimmed fastq> <untrimmed fastq> <trimmer log> <nb_raw> <nb_adapt> <nb_adapt_deduped> <nb_noadapt> <nb_noadapt_deduped>
 
 # http://linuxcommand.org/wss0150.php
 PROGNAME=$(basename $0)
@@ -18,27 +18,26 @@ function error_exit
 # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in
 #PACKAGEDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
-raw_in=${1}
+trimmer=${1}
 
-adapt=${2}
+raw_in=${2}
 
-fiveprime_random=${3}
-threeprime_random=${4}
+adapt=${3}
 
-trimmed_and_dedup_out=${5}
+fiveprime_random=${4}
+threeprime_random=${5}
 
-untrimmed_out=${6}
+trimmed_and_dedup_out=${6}
 
-log=${7}
+untrimmed_out=${7}
 
-nb_raw=${8}
-nb_adapt=${9}
-nb_adapt_deduped=${10}
-nb_noadapt=${11}
-nb_noadapt_deduped=${12}
+log=${8}
 
-# This script performs 2 sorting and deduplicating operations, depending on the
-# presence or absence of the adapter in the read.
+nb_raw=${9}
+nb_adapt=${10}
+nb_adapt_deduped=${11}
+nb_noadapt=${12}
+nb_noadapt_deduped=${13}
 
 count_fastq_reads()
 {
@@ -46,6 +45,9 @@ count_fastq_reads()
     wc -l | { read nblines; echo ${nblines} / 4 | bc > ${1}; }
 }
 
+# This script performs 2 sorting and deduplicating operations, depending on the
+# presence or absence of the adapter in the read.
+
 
 # The -s option of fastq-sort sorts the reads by their sequence.
 sort_by_seq()
@@ -67,7 +69,7 @@ trim_random_nt()
 {
     # $1: nb of bases to trim at 5' end
     # $2: nb of bases to trim at 3' end
-    cutadapt -u ${1} -u -${2} - || error_exit "trim_random_nt failed"
+    cutadapt -u ${1} -u -${2} - 2> /dev/null || error_exit "trim_random_nt failed"
 }
 
 
@@ -76,14 +78,31 @@ trim_random_nt()
 # second sorting and deduplicating.
 mkfifo ${untrimmed_out}.fifo
 
-minsize_trimmed=$(echo "${fiveprime_random} + 20 + ${threeprime_random}" | bc)
+minsize_trimmed=$(echo "${fiveprime_random} + 16 + ${threeprime_random}" | bc)
+
+case "${trimmer}" in
+    "cutadapt")
         # -m ${minsize_random} is to discard reads that are shorter than this after trimming
+        trim_cmd="${trimmer} -a ${adapt} -m ${minsize_trimmed} --untrimmed-output=${untrimmed_out}.fifo - 2> ${log}"
+        ;;
+    "fastx_clipper")
+        # -l is equivalent to -m in cutadapt (not sure it has effect with -C)
+        # -c is to keep only the trimmed reads
+        # -C is to keep only the non-trimmed reads
+        # -v is to have verbose things to put in the log
+        trim_cmd="tee >(${trimmer} -a ${adapt} -l ${minsize_trimmed} -C -M 3 > ${untrimmed_out}.fifo) | ${trimmer} -a ${adapt} -l ${minsize_trimmed} -v -c -M 3 2>> ${log}"
+        ;;
+    *)
+        error_exit "Trimming adapter with ${trimmer} not implemented."
+        ;;
+esac
+
 # a second cutadapt step removes the random nucleotides that helped identify PCR duplicates.
 dedup_trimmed()
 {
     # $1: file in which to write the number of fastq records after adapter trimming
     # $2: file in which to write the number of fastq records after deduplication
-    cmd="cutadapt -a ${adapt} -m ${minsize_trimmed} --untrimmed-output=${untrimmed_out}.fifo - 2> ${log} | tee >(count_fastq_reads ${1}) | dedup | trim_random_nt ${fiveprime_random} ${threeprime_random} | tee >(count_fastq_reads ${2}) | gzip"
+    cmd="${trim_cmd} | tee >(count_fastq_reads ${1}) | dedup | trim_random_nt ${fiveprime_random} ${threeprime_random} | tee >(count_fastq_reads ${2}) | gzip"
     echo ${cmd}
     eval ${cmd} > ${trimmed_and_dedup_out} || error_exit "${cmd} failed"
 }
@@ -99,9 +118,11 @@ dedup_untrimmed()
 zcat ${raw_in} \
     | tee >(count_fastq_reads ${nb_raw}) \
     | dedup_trimmed ${nb_adapt} ${nb_adapt_deduped} &
+pid_to_wait=$!
 cat ${untrimmed_out}.fifo \
     | tee >(count_fastq_reads ${nb_noadapt}) \
     | dedup_untrimmed ${nb_noadapt_deduped} || rm -f ${untrimmed_out}.fifo
+wait ${pid_to_wait}
 rm -f ${untrimmed_out}.fifo
 
 exit 0