Build branch main with version main (32dc807)

Build pipeline: viash-hub.playground.main-n876l

Source commit: 32dc80723a

Source message: Emtpy commit

_viash.yaml

@@ -7,7 +7,7 @@ links:
   issue_tracker: https://github.com/viash-hub/playground/issues
   repository: https://github.com/viash-hub/playground
 
-viash_version: 0.9.0-RC6
+viash_version: 0.9.0
 
 config_mods: |
   .requirements.commands := ['ps']

src/mapping_and_qc/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: mapping_and_qc
 description: Run STAR and QC
+
 argument_groups:
   - name: Input arguments
     arguments:
@@ -27,7 +28,6 @@ resources:
     path: main.nf
     entrypoint: run_wf
 
-
 dependencies:
   - name: cutadapt
     repository: bb
@@ -45,6 +45,7 @@ repositories:
     type: vsh
     repo: vsh/biobox
     tag: main
+
 runners:
   - type: nextflow
 

target/nextflow/mapping_and_qc/.config.vsh.yaml

@@ -161,8 +161,8 @@ build_info:
   engine: "native|native"
   output: "target/nextflow/mapping_and_qc"
   executable: "target/nextflow/mapping_and_qc/main.nf"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
-  git_commit: "d87d344d4e46dc6f938e57a009607946ed31447c"
+  git_commit: "32dc80723acb5d5861c7acd7c6c07ef4cd1a6ee7"
   git_remote: "https://github.com/viash-hub/playground"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/cutadapt"
@@ -176,7 +176,7 @@ package_config:
   description: "A collection of bioinformatics pipelines to illustrate the use of\
     \ biobox (and biotools).\n"
   info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
   source: "src"
   target: "target"
   config_mods:

target/nextflow/mapping_and_qc/main.nf

@@ -1,8 +1,8 @@
 // mapping_and_qc main
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
-// Data Intuitive.
+// 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
@@ -760,8 +760,11 @@ def runEach(Map args) {
   def fromState_ = args.fromState
   def toState_ = args.toState
   def filter_ = args.filter
+  def runIf_ = args.runIf
   def id_ = args.id
 
+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
   workflow runEachWf {
     take: input_ch
     main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
           [new_id] + tup.drop(1)
         }
         : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
           def new_data = tup[1]
           if (fromState_ instanceof Map) {
             new_data = fromState_.collectEntries{ key0, key1 ->
@@ -822,7 +838,10 @@ def runEach(Map args) {
         }
         : out_ch
 
-      post_ch
+      def return_ch = post_ch
+        | concat(chPassthrough)
+      
+      return_ch
     }
 
     // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
           // construct renameMap
           if (args.rename_keys) {
             def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
+              def split = renameString.split(":")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
               split
             }
 
@@ -1709,7 +1728,9 @@ 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_?
 
@@ -1780,7 +1801,9 @@ 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
@@ -1822,7 +1845,9 @@ 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
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         tuple
       }
 
-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified
 
     def chRun = null
     def chPassthrough = null
     if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
         run: workflowArgs.runIf(tup[0], tup[1])
         passthrough: true
       }
       chRun = runIfBranch.run
       chPassthrough = runIfBranch.passthrough
     } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
       chPassthrough = Channel.empty()
     }
 
+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
     def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
         def new_data = workflowArgs.fromState(it.take(2))
         [it[0], new_data]
       } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}
 
     // fill in defaults
     def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       // | view{"chInitialOutput: ${it.take(3)}"}
 
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2988,15 +3014,15 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/mapping_and_qc",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
-    "git_commit" : "d87d344d4e46dc6f938e57a009607946ed31447c",
+    "git_commit" : "32dc80723acb5d5861c7acd7c6c07ef4cd1a6ee7",
     "git_remote" : "https://github.com/viash-hub/playground"
   },
   "package_config" : {
     "name" : "playground",
     "version" : "main",
     "description" : "A collection of bioinformatics pipelines to illustrate the use of biobox (and biotools).\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
     "source" : "src",
     "target" : "target",
     "config_mods" : [

test_data.sh

@@ -15,18 +15,18 @@ if [ ! -f "$TEST_DATA_DIR/SRR1570800_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR157
   docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1570800
 fi
 
-head -n 10000 "$TEST_DATA_DIR/SRR1569895_1.fastq" > "$TEST_DATA_DIR/SRR1569895_1_subsample.fastq" 
+head -n 10000 "$TEST_DATA_DIR/SRR1569895_1.fastq" >"$TEST_DATA_DIR/SRR1569895_1_subsample.fastq"
-head -n 10000 "$TEST_DATA_DIR/SRR1569895_2.fastq" > "$TEST_DATA_DIR/SRR1569895_2_subsample.fastq"
+head -n 10000 "$TEST_DATA_DIR/SRR1569895_2.fastq" >"$TEST_DATA_DIR/SRR1569895_2_subsample.fastq"
-head -n 10000 "$TEST_DATA_DIR/SRR1570800_1.fastq" > "$TEST_DATA_DIR/SRR1570800_1_subsample.fastq" 
+head -n 10000 "$TEST_DATA_DIR/SRR1570800_1.fastq" >"$TEST_DATA_DIR/SRR1570800_1_subsample.fastq"
-head -n 10000 "$TEST_DATA_DIR/SRR1570800_2.fastq" > "$TEST_DATA_DIR/SRR1570800_2_subsample.fastq" 
+head -n 10000 "$TEST_DATA_DIR/SRR1570800_2.fastq" >"$TEST_DATA_DIR/SRR1570800_2_subsample.fastq"
 
 export NXF_SCM_FILE="$TEST_DATA_DIR/scm.config"
 
-cat > $NXF_SCM_FILE << EOF
+cat >$NXF_SCM_FILE <<EOF
 providers {
     vsh {
         platform = 'gitlab'
-        server = 'https://viash-hub.com/'
+        server = 'https://packages.viash-hub.com/'
     }
 }
 EOF
@@ -44,8 +44,8 @@ if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release" ]; then
     --publish_dir "$TEST_DATA_DIR"
 fi
 
-gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa" 
+gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" >"$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
-gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
+gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" >"$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
 sed -i -e 's/^.*chromosome=\(.*\)\]$/>chr\1/' "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
 
 if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR" ]; then
@@ -61,7 +61,7 @@ if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR" ]; then
 fi
 
 PARAMS_FILE=params_file.yaml
-cat > $PARAMS_FILE << EOF
+cat >$PARAMS_FILE <<EOF
 param_list:
   - id: SRR1569895
     input_r1: $TEST_DATA_DIR/SRR1569895_1_subsample.fastq