change test dataset

src/rsem/rsem_calculate_expression/config.vsh.yaml

@@ -23,7 +23,7 @@ argument_groups:
     description: Sample strand-specificity. Must be one of unstranded, forward, reverse
     choices: [forward, reverse, unstranded]
   - name: "--paired"
-    type: boolean
+    type: boolean_true
     description: Paired-end reads or not?
   - name: "--input"
     type: file

src/rsem/rsem_calculate_expression/script.sh

@@ -25,11 +25,67 @@ IFS=";" read -ra input <<< $par_input
 INDEX=$(find -L $meta_resources_dir/$par_index -name "*.grp" | sed 's/\.grp$//')
 
 rsem-calculate-expression \
+    ${par_quiet:+-q} \
+    ${par_no_bam_output:+--no-bam-output} \
+    ${par_sampling_for_bam:+--sampling-for-bam} \
+    ${par_no_qualities:+--no-qualities} \
+    ${par_alignments:+--alignments} \
+    ${par_bowtie2:+--bowtie2} \
+    ${par_star:+--star} \
+    ${par_hisat2_hca:+--hisat2-hca} \
+    ${par_append_names:+--append-names} \
+    ${par_single_cell_prior:+--single-cell-prior} \
+    ${par_calc_pme:+--calc-pme} \
+    ${par_calc_ci:+--calc-ci} \
+    ${par_phred64_quals:+--phred64-quals} \
+    ${par_solexa_quals:+--solexa-quals} \
+    ${par_star_gzipped_read_file:+--star-gzipped-read-file} \
+    ${par_star_bzipped_read_file:+--star-bzipped-read-file} \
+    ${par_star_output_genome_bam:+--star-output-genome-bam} \
+    ${par_estimate_rspd:+--estimate-rspd} \
+    ${par_keep_intermediate_files:+--keep-intermediate-files} \
+    ${par_time:+--time} \
+    ${par_run_pRSEM:+--run-pRSEM} \
+    ${par_cap_stacked_chipseq_reads:+--cap-stacked-chipseq-reads} \
+    ${par_sort_bam_by_read_name:+--sort-bam-by-read-name} \
+    ${par_counts_gene:+--counts-gene "$par_counts_gene"} \
+    ${par_counts_transcripts:+--counts-transcripts "$par_counts_transcripts"} \
+    ${par_stat:+--stat "$par_stat"} \
+    ${par_bam_star:+--bam-star "\$par_bam_star"} \
+    ${par_bam_genome:+--bam-genome "$par_bam_genome"} \
+    ${par_bam_transcript:+--bam-transcript "$par_bam_transcript"} \
+    ${par_fai:+--fai "$par_fai"} \
+    ${par_seed:+--seed "$par_seed"} \
+    ${par_seed_length:+--seed-length "$par_seed_length"} \
+    ${par_bowtie_n:+--bowtie-n "$par_bowtie_n"} \
+    ${par_bowtie_e:+--bowtie-e "$par_bowtie_e"} \
+    ${par_bowtie_m:+--bowtie-m "$par_bowtie_m"} \
+    ${par_bowtie_chunkmbs:+--bowtie-chunkmbs "$par_bowtie_chunkmbs"} \
+    ${par_bowtie2_mismatch_rate:+--bowtie2-mismatch-rate "$par_bowtie2_mismatch_rate"} \
+    ${par_bowtie2_k:+--bowtie2-k "$par_bowtie2_k"} \
+    ${par_bowtie2_sensitivity_level:+--bowtie2-sensitivity-level "$par_bowtie2_sensitivity_level"} \
+    ${par_tag:+--tag "$par_tag"} \
+    ${par_fragment_length_min:+--fragment-length-min "$par_fragment_length_min"} \
+    ${par_fragment_length_max:+--fragment-length-max "$par_fragment_length_max"} \
+    ${par_fragment_length_mean:+--fragment-length-mean "$par_fragment_length_mean"} \
+    ${par_fragment_length_sd:+--fragment-length-sd "$par_fragment_length_sd"} \
+    ${par_num_rspd_bins:+--num-rspd-bins "$par_num_rspd_bins"} \
+    ${par_gibbs_burnin:+--gibbs-burnin "$par_gibbs_burnin"} \
+    ${par_gibbs_number_of_samples:+--gibbs-number-of-samples "$par_gibbs_number_of_samples"} \
+    ${par_gibbs_sampling_gap:+--gibbs-sampling-gap "$par_gibbs_sampling_gap"} \
+    ${par_ci_credibility_level:+--ci-credibility-level "$par_ci_credibility_level"} \
+    ${par_ci_number_of_samples_per_count_vector:+--ci-number-of-samples-per-count-vector "$par_ci_number_of_samples_per_count_vector"} \
+    ${par_temporary_folder:+--temporary-folder "$par_temporary_folder"} \
+    ${par_chipseq_peak_file:+--chipseq-peak-file "$par_chipseq_peak_file"} \
+    ${par_chipseq_target_read_files:+--chipseq-target-read-files "$par_chipseq_target_read_files"} \
+    ${par_chipseq_control_read_files:+--chipseq-control-read-files "$par_chipseq_control_read_files"} \
+    ${par_chipseq_read_files_multi_targets:+--chipseq-read-files-multi-targets "$par_chipseq_read_files_multi_targets"} \
+    ${par_chipseq_bed_files_multi_targets:+--chipseq-bed-files-multi-targets "$par_chipseq_bed_files_multi_targets"} \
+    ${par_n_max_stacked_chipseq_reads:+--n-max-stacked-chipseq-reads "$par_n_max_stacked_chipseq_reads"} \
+    ${par_partition_model:+--partition-model "$par_partition_model"} \
     $strandedness \
     ${par_paired:+--paired-end} \
-    $par_extra_args \
     ${input[*]} \
     $INDEX \
-    $par_id \
-    --quiet
+    $par_id
 

src/rsem/rsem_calculate_expression/test.sh

@@ -3,19 +3,18 @@
 echo ">>> Testing $meta_executable"
 
 test_dir="${meta_resources_dir}/test_data"
+gunzip -k $test_dir/index.tar.gz
+tar -xf $test_dir/index.tar
 
-gunzip "${test_dir}/rsem.tar.gz"
-tar -xf "${test_dir}/rsem.tar"
-
-echo ">>> Calculating expression"
+echo ">>> Test 1: Paired-end reads using STAR to align reads"
 "$meta_executable" \
-  --id WT_REP1 \
+  --id mmliver \
   --strandedness reverse \
-  --paired true \
-  --input "${test_dir}/SRR6357070_1.fastq.gz;${test_dir}/SRR6357070_2.fastq.gz" \
-  --index rsem \
-  --extra_args "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" \
-  --logs WT_REP1.log \
+  --paired \
+  --input "${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
 
 echo ">>> Checking whether output exists"
 [ ! -f "WT_REP1.genes.results" ] && echo "Gene level expression counts file does not exist!" && exit 1
@@ -30,23 +29,27 @@ echo ">>> Checking whether output exists"
 
 ####################################################################################################
 
-echo ">>> Test 2: Single-end reads without quality scores"
-"$meta_executable" \
-  --no-qualities \
-  --input "${test_dir}/SRR6357070_1.fastq.gz" \
-  --index rsem \
-  --id WT_REP1_no_qual
-
-####################################################################################################
-
-echo ">>> Test 3: Paired-end reads with quality scores, using STAR to align reads"
-"$meta_executable" \
-  --star \
-  --star-gzipped-read-file \
-  --paired-end \
-  --input "${test_dir}/SRR6357070_1.fastq.gz;${test_dir}/SRR6357070_2.fastq.gz" \
-  --index rsem \
-  WT_REP1_star
+# echo ">>> Test 2: Single-end reads without quality scores"
+# "$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
 
 echo "All tests succeeded!"
 exit 0