Build branch main with version main (38f635a)

Build pipeline: viash-hub.biobox.main-dz9k8 Source commit: 38f635ad57 Source message: Add agat convert genscan2gff (#100) * add config * add help * add test data and expected output adn the script to obtain them * add running script * add test script * update changelog * cleanup * fix tests * format description * remove unused argument --inflate-off * update --config description * add requirements * create temporary directory and clean up on exit * add GENSCAN in keywords * add set -e to test * fix create temporary directory * add set -eo pipefail to test * add set -eo pipefail to script * fix create temporary directory * update --config description * cleanup changelog * cleanup changelog * Update deprecated variable --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
2024-09-17 07:19:20 +00:00
parent 4b61e09a56
commit f47054953e
255 changed files with 8531 additions and 1561 deletions
--- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
@@ -184,15 +184,16 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/bcftools/bcftools_sort"
  executable: "target/nextflow/bcftools/bcftools_sort/main.nf"
-  viash_version: "0.9.0-RC7"
-  git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
-  git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+  viash_version: "0.9.0"
+  git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
+  git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-2-g38f635a"
 package_config:
  name: "biobox"
  version: "main"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/bcftools/bcftools_sort/main.nf
+++ b/target/nextflow/bcftools/bcftools_sort/main.nf
@@ -1,8 +1,8 @@
 // bcftools_sort main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -1731,7 +1731,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1802,7 +1804,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)
          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()

          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1844,7 +1848,9 @@ def publishStatesByConfig(Map args) {
                // instantiate the template
                def filename = filenameTemplate
                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
                if (par.multiple) {
                  // if the parameter is multiple: true, the filename
                  // should contain a wildcard '*' that is replaced with
@@ -3041,15 +3047,16 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/bcftools/bcftools_sort",
-    "viash_version" : "0.9.0-RC7",
-    "git_commit" : "124d50ce5318b612e4a1e4da1be705523cd6eab7",
-    "git_remote" : "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
+    "viash_version" : "0.9.0",
+    "git_commit" : "38f635ad57ef05550bba3a0864c81627f84f5ad2",
+    "git_remote" : "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-2-g38f635a"
  },
  "package_config" : {
    "name" : "biobox",
    "version" : "main",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0-RC7",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3200,7 +3207,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3331,7 +3342,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3339,8 +3351,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3377,6 +3389,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3388,10 +3401,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports