expected output (not correct) and update to R script package installa…

…tion

src/dupradar/config.vsh.yaml

@@ -38,43 +38,41 @@ argument_groups:
     type: file
     direction: output
     description: path to output file (txt) of duplicate tag counts
-    example: $id.dup_matrix.txt
+    example: dup_matrix.txt
   - name: --output_dup_intercept_mqc
     type: file
     direction: output
     description: path to output file (txt) of multiqc intercept value DupRadar
-    example: $id.dup_intercept_mqc.txt
+    example: dup_intercept_mqc.txt
   - name: --output_duprate_exp_boxplot
     type: file
     direction: output
-    required: false
-    must_exist: true
-    default: $id.duprate_exp_boxplot.pdf
+    default: duprate_exp_boxplot.pdf
     description: |
       Path to output file (pdf) of distribution of expression box plot
   - name: --output_duprate_exp_densplot
     type: file
     direction: output
     description: |
       Path to output file (pdf) of 2D density scatter plot of duplicate tag counts
-    example: $id.duprate_exp_densityplot.pdf
+    example: duprate_exp_densityplot.pdf
   - name: --output_duprate_exp_denscurve_mqc
     type: file
     direction: output
     description: |
       Path to output file (pdf) of density curve of gene duplication multiqc
-    example: $id.duprate_exp_density_curve_mqc.txt
+    example: duprate_exp_density_curve_mqc.txt
   - name: --output_expression_histogram
     type: file
     direction: output
     description: |
       Path to output file (pdf) of distribution of RPK values per gene histogram
-    example: $id.expression_hist.pdf
+    example: expression_hist.pdf
   - name: --output_intercept_slope
     type: file
     direction: output
     description: output file (txt) with progression of duplication rate values
-    example: $id.intercept_slope.txt
+    example: intercept_slope.txt
 
 resources:
   - type: bash_script
@@ -85,6 +83,8 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
+  - type: file
+    path: test_data
 engines:
   - type: docker
     image: quay.io/biocontainers/bioconductor-dupradar:1.32.0--r43hdfd78af_0

src/dupradar/script.R

@@ -35,10 +35,12 @@ message("R package loc. (Arg 7): ", ifelse(length(args) > 4, args[5], "Not speci
 
 # Load / install packages
 if (length(args) > 5) { .libPaths( c( args[6], .libPaths() ) ) }
-if (!require("dupRadar")){
-    source("http://bioconductor.org/biocLite.R")
-    biocLite("dupRadar", suppressUpdates=TRUE)
-    library("dupRadar")
+if (!require("dupRadar")) {
+  if (!requireNamespace("BiocManager", quietly = TRUE)) {
+    install.packages("BiocManager")
+  }
+  BiocManager::install("dupRadar", update = TRUE, ask=FALSE)
+  library("dupRadar")
 }
 if (!require("parallel")) {
     install.packages("parallel", dependencies=TRUE, repos='http://cloud.r-project.org/')

src/dupradar/script.sh

@@ -19,7 +19,8 @@ Rscript "$meta_resources_dir/script.R" \
     $par_id \
     $par_gtf_annotation \
     $(num_strandness) \
-    $par_paired
+    $par_paired \
+    ${meta_cpus:-1}
 
 mv "$par_id"_dupMatrix.txt $par_output_dupmatrix
 mv "$par_id"_dup_intercept_mqc.txt $par_output_dup_intercept_mqc

src/dupradar/test.sh

@@ -1,8 +1,8 @@
 #!/bin/bash
 
 # define input and output for script
-input_bam="$meta_resources_dir/sample.bam"
-input_gtf="$meta_resources_dir/genes.gtf"
+input_bam="${meta_resources_dir}/test_data/sample.bam"
+input_gtf="${meta_resources_dir}/test_data/genes.gtf"
 
 output_dupmatrix="dup_matrix.txt"
 output_dup_intercept_mqc="dup_intercept_mqc.txt"
@@ -48,4 +48,24 @@ echo ">> asserting output has been created for paired read input"
 [ ! -f "$output_intercept_slope" ] && echo "$output_intercept_slope was not created" && exit 1
 [ ! -s "$output_intercept_slope" ] && echo "$output_intercept_slope is empty" && exit 1
 
+
+echo ">> Check if output is empty"
+[ ! -s "$output_dupmatrix" ] \
+    && echo "Output file $output_dupmatrix is empty" && exit 1
+[ ! -s "$output_dup_intercept_mqc" ] \
+    && echo "Output file $output_dup_intercept_mqc is empty" && exit 1
+[ ! -s "$output_intercept_slope" ] \
+    && echo "Output file $output_intercept_slope is empty" && exit 1
+
+echo ">> Check if output is correct"
+cat "$output_dupmatrix"
+cat "$output_dup_intercept_mqc"
+cat "$output_intercept_slope"
+# diff ignoring white spaces
+diff -B -b "test_dupMatrix.pdf" "${meta_resources_dir}/test_data/test_dupMatrix.txt" || 
+    (echo "Output file $output_dupmatrix is not correct" && exit 1)
+diff -B -b "$output_dup_intercept_mqc" "${meta_resources_dir}/test_data/test_duprateExpDensCurve_mqc.txt" || \
+    (echo "Output file $output_dup_intercept_mqc is not correct" && exit 1)
+diff -B -b "$output_intercept_slope" "${meta_resources_dir}/test_data/test_intercept_slope.txt" || \
+    (echo "Output file $output_intercept_slope is not correct" && exit 1)
 exit 0

src/dupradar/test_data/test_dupMatrix.txt

@@ -0,0 +1,7 @@
+ID	geneLength	allCountsMulti	filteredCountsMulti	dupRateMulti	dupsPerIdMulti	RPKMulti	PKMMulti	allCounts	filteredCounts	dupRate	dupsPerId	RPK	RPKM
+WASH7P	1769	41	41	0	0	23.1769361221029	188430.374976446	1	1	0	0	0.565291124929339	4595.86280430357
+FAM138A	2260	0	0	NA	0	0	0	0	0	NA	0	0	0
+FAM138F	2260	0	0	NA	0	0	0	0	0	NA	0	0	0
+OR4F5	918	0	0	NA	0	0	0	0	0	NA	0	0	0
+LOC729737	5474	18	18	0	0	3.28827183047132	26733.917320905	3	3	0	0	0.548045305078553	4455.65288681751
+LOC100132287	8740	39	39	0	0	4.46224256292906	36278.3948205615	1	1	0	0	0.11441647597254	930.215251809269

src/dupradar/test_data/test_dup_intercept_mqc.txt

@@ -0,0 +1,39 @@
+#id: DupInt
+#plot_type: 'generalstats'
+#pconfig:
+#    dupRadar_intercept:
+#        title: 'dupInt'
+#        namespace: 'DupRadar'
+#        description: 'Intercept value from DupRadar'
+#        max: 100
+#        min: 0
+#        scale: 'RdYlGn-rev'
+#        format: '{:.2f}%'
+Sample dupRadar_intercept
+test 5.8262146393079e-11
+#id: DupInt
+#plot_type: 'generalstats'
+#pconfig:
+#    dupRadar_intercept:
+#        title: 'dupInt'
+#        namespace: 'DupRadar'
+#        description: 'Intercept value from DupRadar'
+#        max: 100
+#        min: 0
+#        scale: 'RdYlGn-rev'
+#        format: '{:.2f}%'
+Sample dupRadar_intercept
+test 5.8262146393079e-11
+#id: DupInt
+#plot_type: 'generalstats'
+#pconfig:
+#    dupRadar_intercept:
+#        title: 'dupInt'
+#        namespace: 'DupRadar'
+#        description: 'Intercept value from DupRadar'
+#        max: 100
+#        min: 0
+#        scale: 'RdYlGn-rev'
+#        format: '{:.2f}%'
+Sample dupRadar_intercept
+test 5.8262146393079e-11

src/dupradar/test_data/test_duprateExpDensCurve_mqc.txt

@@ -0,0 +1,33 @@
+#id: dupradar
+#section_name: 'DupRadar'
+#section_href: 'bioconductor.org/packages/release/bioc/html/dupRadar.html'
+#description: "provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication.
+#    This plot shows the general linear models - a summary of the gene duplication distributions. "
+#pconfig:
+#    title: 'DupRadar General Linear Model'
+#    xLog: True
+#    xlab: 'expression (reads/kbp)'
+#    ylab: '% duplicate reads'
+#    ymax: 100
+#    ymin: 0
+#    tt_label: '<b>{point.x:.1f} reads/kbp</b>: {point.y:,.2f}% duplicates'
+#    xPlotLines:
+#        - color: 'green'
+#          dashStyle: 'LongDash'
+#          label:
+#                style: {color: 'green'}
+#                text: '0.5 RPKM'
+#                verticalAlign: 'bottom'
+#                y: -65
+#          value: 0.5
+#          width: 1
+#        - color: 'red'
+#          dashStyle: 'LongDash'
+#          label:
+#                style: {color: 'red'}
+#                text: '1 read/bp'
+#                verticalAlign: 'bottom'
+#                y: -65
+#          value: 1000
+#          width: 1
+0.11441647597254 5.82621463896864e-09

src/dupradar/test_data/test_intercept_slope.txt

@@ -0,0 +1,2 @@
+test - dupRadar Int (duprate at low read counts): 5.8262146393079e-11 
+test - dupRadar Sl (progression of the duplication rate): 0.999999999999966