functional test, adjustements to scripts

src/rsem/rsem_calculate_expression/script.sh

@@ -12,9 +12,9 @@ trap clean_up EXIT
 
 tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
 
-if [ $par_strandedness == 'forward' ]; then
+if [ "$par_strandedness" == 'forward' ]; then
     strandedness='--strandedness forward'
-elif [ $par_strandedness == 'reverse' ]; then
+elif [ "$par_strandedness" == 'reverse' ]; then
     strandedness="--strandedness reverse"
 else
     strandedness=''
@@ -24,6 +24,18 @@ IFS=";" read -ra input <<< $par_input
 
 INDEX=$(find -L $meta_resources_dir/$par_index -name "*.grp" | sed 's/\.grp$//')
 
+unset_if_false=( par_paired par_quiet par_no_bam_output par_sampling_for_bam par_no_qualities 
+                 par_alignments par_bowtie2 par_star par_hisat2_hca par_append_names 
+                 par_single_cell_prior par_calc_pme par_calc_ci par_phred64_quals 
+                 par_solexa_quals par_star_gzipped_read_file par_star_bzipped_read_file 
+                 par_star_output_genome_bam par_estimate_rspd par_keep_intermediate_files 
+                 par_time par_run_pRSEM par_cap_stacked_chipseq_reads par_sort_bam_by_read_name )
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
 rsem-calculate-expression \
     ${par_quiet:+-q} \
     ${par_no_bam_output:+--no-bam-output} \

src/rsem/rsem_calculate_expression/test.sh

@@ -3,53 +3,37 @@
 echo ">>> Testing $meta_executable"
 
 test_dir="${meta_resources_dir}/test_data"
-gunzip -k $test_dir/index.tar.gz
-tar -xf $test_dir/index.tar
+
+wget https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz
+gunzip -k rsem.tar.gz
+tar -xf rsem.tar
+
+mv $test_dir/rsem $meta_resources_dir
 
 echo ">>> Test 1: Paired-end reads using STAR to align reads"
 "$meta_executable" \
-  --id mmliver \
-  --strandedness reverse \
-  --paired \
-  --input "${test_dir}/mmliver_1.fq.gz;${test_dir}/mmliver_2.fq.gz" \
-  --index index \
-  --star --star_output_genome_bam --star_gzipped_read_file --estimate_rspd --seed 1 \
-  --quiet
+    --star \
+    --star_gzipped_read_file \
+    --paired \
+    --input "$test_dir/SRR6357070_1.fastq.gz;$test_dir/SRR6357070_2.fastq.gz" \
+    --index rsem \
+    --id WT_REP1 \
+    --seed 1 \
+    --quiet
 
 echo ">>> Checking whether output exists"
 [ ! -f "WT_REP1.genes.results" ] && echo "Gene level expression counts file does not exist!" && exit 1
 [ ! -s "WT_REP1.genes.results" ] && echo "Gene level expression counts file is empty!" && exit 1
 [ ! -f "WT_REP1.isoforms.results" ] && echo "Transcript level expression counts file does not exist!" && exit 1
 [ ! -s "WT_REP1.isoforms.results" ] && echo "Transcript level expression counts file is empty!" && exit 1
-[ ! -f "WT_REP1.stat" ] && echo "Stats file does not exist!" && exit 1
-[ ! -s "WT_REP1.stat" ] && echo "Stats file is empty!" && exit 1
-[ ! -f "WT_REP1.log" ] && echo "Log file does not exist!" && exit 1
-[ ! -s "WT_REP1.log" ] && echo "Log file is empty!" && exit 1
-
-
-####################################################################################################
-
-# echo ">>> Test 2: Single-end reads without quality scores"
-# "$meta_executable" \
-#   --phred64-quals \
-#   --append-names \
-#   --output-genome-bam \
-#   --input /$test_dir/mmliver_1.fq \
-#   --index index \
-#   --id mmliver_single_quals
-
-# ####################################################################################################
-
-# echo ">>> Test 3: Paired-end reads with quality scores, using STAR to align reads"
-# "$meta_executable" \
-#   --phred64-quals \
-#   --fragment-length-mean 150.0 \
-#   --fragment-length-sd 35.0 \
-#   --output-genome-bam \
-#   --calc-ci \
-#   --input /$test_dir/mmliver.fq \
-#   --index index \
-#   --id mmliver_single_quals
+[ ! -d "WT_REP1.stat" ] && echo "Stats file does not exist!" && exit 1
+
+echo ">>> Check wheter output is correct"
+diff $test_dir/ref.genes.results WT_REP1.genes.results || { echo "Gene level expression counts file is incorrect!"; exit 1; }
+diff $test_dir/ref.isoforms.results WT_REP1.isoforms.results || { echo "Transcript level expression counts file is incorrect!"; exit 1; }
+diff $test_dir/ref.cnt WT_REP1.stat/WT_REP1.cnt || { echo "Stats file is incorrect!"; exit 1; }
+
+#####################################################################################################
 
 echo "All tests succeeded!"
 exit 0