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Build branch main with version main (9f37358)

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Build pipeline: viash-hub.demultiplex.main-f597w

Source commit: 9f37358ebf

Source message: Minor adjustments to CHANGELOG and README (#45)
This commit is contained in:
CI
2025-04-25 12:20:54 +00:00
parent eb6fd9e999
commit 60ee0cd261
30 changed files with 388 additions and 411 deletions
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10
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -164,10 +164,10 @@ build_info:
engine: "native|native"
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.3"
git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
viash_version: "0.9.4"
git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-22-g162497a"
git_tag: "v0.1.1-24-g9f37358"
package_config:
name: "demultiplex"
version: "main"
@@ -176,11 +176,11 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/demultiplex/v2/"
dest: "testData"
viash_version: "0.9.3"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
- ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
\ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
)'\n"

77
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -1,6 +1,6 @@
// combine_samples main
//
// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
// Intuitive.
//
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
foundClass = "List[${e.foundClass}]"
}
} else if (par.type == "string") {
// cast to string if need be
// cast to string if need be. only cast if the value is a GString
if (value instanceof GString) {
value = value.toString()
value = value as String
}
expectedClass = value instanceof String ? null : "String"
} else if (par.type == "integer") {
// cast to integer if need be
if (value instanceof String) {
if (value !instanceof Integer) {
try {
value = value.toInteger()
value = value as Integer
} catch (NumberFormatException e) {
// do nothing
expectedClass = "Integer"
}
}
if (value instanceof java.math.BigInteger) {
value = value.intValue()
}
expectedClass = value instanceof Integer ? null : "Integer"
} else if (par.type == "long") {
// cast to long if need be
if (value instanceof String) {
if (value !instanceof Long) {
try {
value = value.toLong()
value = value as Long
} catch (NumberFormatException e) {
// do nothing
expectedClass = "Long"
}
}
if (value instanceof Integer) {
value = value.toLong()
}
expectedClass = value instanceof Long ? null : "Long"
} else if (par.type == "double") {
// cast to double if need be
if (value instanceof String) {
if (value !instanceof Double) {
try {
value = value.toDouble()
value = value as Double
} catch (NumberFormatException e) {
// do nothing
expectedClass = "Double"
}
}
if (value instanceof java.math.BigDecimal) {
value = value.doubleValue()
} else if (par.type == "float") {
// cast to float if need be
if (value !instanceof Float) {
try {
value = value as Float
} catch (NumberFormatException e) {
expectedClass = "Float"
}
}
if (value instanceof Float) {
value = value.toDouble()
}
expectedClass = value instanceof Double ? null : "Double"
} else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
// cast to boolean if need be
if (value instanceof String) {
def valueLower = value.toLowerCase()
if (valueLower == "true") {
value = true
} else if (valueLower == "false") {
value = false
if (value !instanceof Boolean) {
try {
value = value as Boolean
} catch (Exception e) {
expectedClass = "Boolean"
}
}
expectedClass = value instanceof Boolean ? null : "Boolean"
} else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
// cast to path if need be
if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
expectedClass = value instanceof Path ? null : "Path"
} else if (par.type == "file" && stage == "input" && par.direction == "output") {
// cast to string if need be
if (value instanceof GString) {
value = value.toString()
if (value !instanceof String) {
try {
value = value as String
} catch (Exception e) {
expectedClass = "String"
}
}
expectedClass = value instanceof String ? null : "String"
} else {
// didn't find a match for par.type
expectedClass = par.type
@@ -3234,10 +3229,10 @@ meta = [
"runner" : "nextflow",
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.3",
"git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
"viash_version" : "0.9.4",
"git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-22-g162497a"
"git_tag" : "v0.1.1-24-g9f37358"
},
"package_config" : {
"name" : "demultiplex",
@@ -3251,11 +3246,11 @@ meta = [
}
]
},
"viash_version" : "0.9.3",
"viash_version" : "0.9.4",
"source" : "src",
"target" : "target",
"config_mods" : [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'main'"

18
target/nextflow/dataflow/combine_samples/nextflow_schema.json
View File

@@ -67,10 +67,10 @@
"output_forward": {
"type":
"string",
"description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. "
"description": "Type: List of `file`, required, default: `$id.$key.output_forward_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*`, multiple_sep: `\";\"`. "
,
"default":"$id.$key.output_forward_*.output_forward_*"
"default":"$id.$key.output_forward_*"
}
@@ -78,10 +78,10 @@
"output_reverse": {
"type":
"string",
"description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. "
"description": "Type: List of `file`, default: `$id.$key.output_reverse_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*`, multiple_sep: `\";\"`. "
,
"default":"$id.$key.output_reverse_*.output_reverse_*"
"default":"$id.$key.output_reverse_*"
}
@@ -89,10 +89,10 @@
"output_falco": {
"type":
"string",
"description": "Type: List of `file`, required, default: `$id.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. "
"description": "Type: List of `file`, required, default: `$id.$key.output_falco_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_falco_*`, multiple_sep: `\";\"`. "
,
"default":"$id.$key.output_falco_*.output_falco_*"
"default":"$id.$key.output_falco_*"
}