Allow multiple for adapters/fasta and add test

src/cutadapt/config.vsh.yaml

@@ -53,6 +53,7 @@ functionality:
       arguments:
         - name: --adapter_fasta
           type: file
+          multiple: true
           description: |
             Fasta file containing sequences of an adapter ligated to the 3' end (paired data:
             of the first read). The adapter and subsequent bases are

src/cutadapt/script.sh

@@ -28,20 +28,82 @@ fi
 #   - paired and single-end
 #   - string and fasta
 ###########################################################
+
+multi_adapter=""
+for adapter in `echo $par_adapter | tr ':' ' '`; do
+  multi_adapter="$multi_adapter --adapter $adapter"
+done
+
+multi_adapter_fasta=""
+for adapter_fasta in `echo $par_adapter_fasta | tr ':' ' '`; do
+  multi_adapter_fasta="$multi_adapter_fasta --adapter file:$adapter_fasta"
+done
+
+multi_adapter_r2=""
+for adapter_r2 in `echo $par_adapter_r2 | tr ':' ' '`; do
+  multi_adapter_r2="$multi_adapter_r2 --adapter_r2 $adapter_r2"
+done
+
+multi_adapter_fasta_r2=""
+for adapter_fasta_r2 in `echo $par_adapter_fasta_r2 | tr ':' ' '`; do
+  multi_adapter_fasta_r2="$multi_adapter_fasta_r2 --adapter file:$adapter_fasta_r2"
+done
+
+multi_front=""
+for front in `echo $par_front | tr ':' ' '`; do
+  multi_front="$multi_front --front $front"
+done
+
+multi_front_fasta=""
+for front_fasta in `echo $par_front_fasta | tr ':' ' '`; do
+  multi_front_fasta="$multi_front_fasta --front file:$front_fasta"
+done
+
+multi_front_r2=""
+for front_r2 in `echo $par_front_r2 | tr ':' ' '`; do
+  multi_front_r2="$multi_front_r2 --front_r2 $front_r2"
+done
+
+multi_front_fasta_r2=""
+for front_fasta_r2 in `echo $par_front_fasta_r2 | tr ':' ' '`; do
+  multi_front_fasta_r2="$multi_front_fasta_r2 --front file:$front_fasta_r2"
+done
+
+multi_anywhere=""
+for anywhere in `echo $par_anywhere | tr ':' ' '`; do
+  multi_anywhere="$multi_anywhere --anywhere $anywhere"
+done
+
+multi_anywhere_fasta=""
+for anywhere_fasta in `echo $par_anywhere_fasta | tr ':' ' '`; do
+  multi_anywhere_fasta="$multi_anywhere_fasta --anywhere file:$anywhere_fasta"
+done
+
+multi_anywhere_r2=""
+for anywhere_r2 in `echo $par_anywhere_r2 | tr ':' ' '`; do
+  multi_anywhere_r2="$multi_anywhere_r2 --anywhere_r2 $anywhere_r2"
+done
+
+multi_anywhere_fasta_r2=""
+for anywhere_fasta_r2 in `echo $par_anywhere_fasta_r2 | tr ':' ' '`; do
+  multi_anywhere_fasta_r2="$multi_anywhere_fasta_r2 --anywhere file:$anywhere_fasta_r2"
+done
+
 echo ">> Parsing arguments dealing with adapters"
 adapter_args=$(echo \
-  ${par_adapter:+--adapter "${par_adapter}"} \
-  ${par_adapter_fasta:+--adapter "file:${par_adapter_fasta}"} \
-  ${par_front:+--front "${par_front}"} \
-  ${par_front_fasta:+--front "file:${par_front_fasta}"} \
-  ${par_anywhere:+--anywhere "${par_anywhere}"} \
-  ${par_anywhere_fasta:+--anywhere "file:${par_anywhere_fasta}"} \
-  ${par_adapter_r2:+--adapter_r2 "${par_adapter_r2}"} \
-  ${par_adapter_r2_fasta:+--adapter_r2 "file:${par_adapter_r2_fasta}"} \
-  ${par_front_r2:+--front_r2 "${par_front_r2}"} \
-  ${par_front_r2_fasta:+--front_r2 "file:${par_front_r2_fasta}"} \
-  ${par_anywhere_r2:+--anywhere_r2 "${par_anywhere_r2}"} \
-  ${par_anywhere_r2_fasta:+--anywhere_r2 "file:${par_anywhere_r2_fasta}"}
+  ${par_adapter:+${multi_adapter}} \
+  ${par_adapter_fasta:+${multi_adapter_fasta}} \
+  ${par_front:+${multi_front}} \
+  ${par_front_fasta:+${multi_front_fasta}} \
+  ${par_anywhere:+${multi_anywhere}} \
+  ${par_anywhere_fasta:+${multi_anywhere_fasta}} \
+
+  ${par_adapter_r2:+${multi_adapter_r2}} \
+  ${par_adapter_fasta_r2:+${multi_adapter_fasta_r2}} \
+  ${par_front_r2:+${multi_front_r2}} \
+  ${par_front_fasta_r2:+${multi_front_fasta_r2}} \
+  ${par_anywhere_r2:+${multi_anywhere_r2}} \
+  ${par_anywhere_fasta_r2:+${multi_anywhere_fasta_r2}} \
 )
 echo "Arguments to cutadapt:"
 echo "$adapter_args"

src/cutadapt/test.sh

@@ -25,11 +25,44 @@ echo ">> Check if output is empty"
 
 rm -r output-dir
 
+echo "> Run with a combination of inputs"
+
+echo ">adapter1" > adapters1.fasta
+echo "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" >> adapters1.fasta
+
+echo ">adapter1" > adapters2.fasta
+echo "TGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" >> adapters2.fasta
+
+"$meta_executable" \
+  --report minimal \
+  --output output-dir \
+  --adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
+  --adapter GGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
+  --adapter_fasta adapters1.fasta \
+  --adapter_fasta adapters2.fasta \
+  --input $dir_in/se/a.fastq \
+  --quality_cutoff 20 \
+  --json
+
+echo ">> Checking output"
+[ ! -f "output-dir/report.txt" ] && echo "report.txt does not exist" && exit 1
+[ ! -f "output-dir/report.json" ] && echo "report.json does not exist" && exit 1
+[ ! -f "output-dir/1_R1_001.fastq" ] && echo "1_R1_001.fastq does not exist" && exit 1
+[ ! -f "output-dir/unknown_R1_001.fastq" ] && echo "1_R1_001.fastq does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ -s "output-dir/1_R1_001.fastq" ] && echo "1_R1_001.fastq should be empty" && exit 1
+[ ! -s "output-dir/unknown_R1_001.fastq" ] && echo "unkown_R1_001.fastq is empty" && exit 1
+
+rm -r output-dir
+rm adapters?.fasta
+
 echo "> Run cutadapt on paired-end data"
 "$meta_executable" \
   --report minimal \
   --output output-dir \
   --adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
+  --adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAB \
   --input $dir_in/pe/a.1.fastq \
   --input_r2 $dir_in/pe/a.2.fastq \
   --quality_cutoff 20 \

src/cutadapt/test_data/script.sh

@@ -13,3 +13,4 @@ cp -r /tmp/snakemake-wrappers/bio/cutadapt/se/test/reads/* src/cutadapt/test_dat
 cp -r /tmp/snakemake-wrappers/bio/cutadapt/pe/test/reads/* src/cutadapt/test_data/pe
 
 rm -rf /tmp/snakemake-wrappers
+