Merge pull request #57 from Ferlab-Ste-Justine/fix/CLIN-3414-allow-to…

…-pass-exomiser-spring-options

fix: CLIN-2414 allow to pass exomiser spring options in task.ext

CHANGELOG.md

@@ -5,6 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.4.0-dev - [date]
 
+### `Fixed`
+- [#57](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/57) Allow to pass exomiser application properties
+
 ## v2.3.0-dev
 
 ### `Added`

docs/usage.md

@@ -106,6 +106,16 @@ To have the Exomiser step start from the VEP output instead, set the parameter `
 
 Note that the parameter `exomiser_start_from_vep` will be ignored if vep is not specified via the `tools` parameter.
 
+### Exomiser CLI options
+
+We typically allow passing extra arguments in our process scripts via the process `task.ext` directive (`task.ext.args` key).
+
+When using the exomiser process, it's important to distinguish between regular CLI options and options that correspond to properties normally specified in the application.properties file.
+
+Regular CLI options should be added to `task.ext.args`.
+
+Options that correspond to application properties (e.g., typically `--exomiser.some-property=value`) must be added to `task.ext.application_properties_args`. These options need to be grouped at the end of the exomiser command to ensure that regular exomiser cli options are parsed correctly.
+
 ### Customize versions and commands
 
 If needed, it is possible to customize the options passed to the vep command by overriding the ext.args directive for the

modules/local/exomiser/main.nf

@@ -33,6 +33,7 @@ process EXOMISER {
 
     script:
     def args = task.ext.args ?: ''
+    def applicationPropertiesArgs = task.ext.application_properties_args ?: ''
 
     def localFrequencyFileArgs = "" 
     if (localFrequencyPath) {
@@ -67,18 +68,19 @@ process EXOMISER {
     #!/bin/bash -eo pipefail
 
     java -Xmx${avail_mem}M -cp \$( cat /app/jib-classpath-file ) \$( cat /app/jib-main-class-file ) \\
-        ${args} \\
         --vcf ${vcfFile} \\
         --assembly "${params.exomiser_genome}" \\
         --analysis "${analysisFile}" \\
         --sample ${phenoFile} \\
         --output-format=HTML,JSON,TSV_GENE,TSV_VARIANT,VCF \\
+        ${args} \\
         --exomiser.data-directory=/`pwd`/${datadir} \\
         ${localFrequencyFileArgs} \\
         ${remmArgs} \\
         ${caddArgs} \\
         --exomiser.${exomiserGenome}.data-version="${exomiserDataVersion}" \\
-        --exomiser.phenotype.data-version="${exomiserDataVersion}"
+        --exomiser.phenotype.data-version="${exomiserDataVersion}" \\
+        ${applicationPropertiesArgs}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":