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Build branch main with version main (60df288)

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Build pipeline: viash-hub.htrnaseq.main-7kcqt

Source commit: 60df288f92

Source message: Replace ignore parameter with pools (#66)
This commit is contained in:
CI
2025-08-05 14:17:29 +00:00
parent 36bd60bf4c
commit e24f1ffc55
71 changed files with 180 additions and 172 deletions
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4
target/nextflow/utils/concatRuns/.config.vsh.yaml
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@@ -160,9 +160,9 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.4"
git_commit: "5a046ba00351f55ce8e9f524bc329dabda0a7a14"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-12-g5a046ba"
git_tag: "v0.7.2-13-g60df288"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
package_config:

4
target/nextflow/utils/concatRuns/main.nf
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@@ -3229,9 +3229,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "5a046ba00351f55ce8e9f524bc329dabda0a7a14",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-12-g5a046ba"
"git_tag" : "v0.7.2-13-g60df288"
},
"package_config" : {
"name" : "htrnaseq",

10
target/nextflow/utils/listInputDir/.config.vsh.yaml
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@@ -19,11 +19,9 @@ argument_groups:
multiple: false
multiple_sep: ";"
- type: "string"
name: "--ignore"
description: "Pool names to ignore."
name: "--pools"
description: "Pool names to include. By default all pools are selected for analysis."
info: null
default:
- "Undetermined"
required: false
direction: "input"
multiple: true
@@ -171,9 +169,9 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "5a046ba00351f55ce8e9f524bc329dabda0a7a14"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-12-g5a046ba"
git_tag: "v0.7.2-13-g60df288"
package_config:
name: "htrnaseq"
version: "main"

13
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3056,11 +3056,8 @@ meta = [
},
{
"type" : "string",
"name" : "--ignore",
"description" : "Pool names to ignore.",
"default" : [
"Undetermined"
],
"name" : "--pools",
"description" : "Pool names to include. By default all pools are selected for analysis.",
"required" : false,
"direction" : "input",
"multiple" : true,
@@ -3239,9 +3236,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "5a046ba00351f55ce8e9f524bc329dabda0a7a14",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-12-g5a046ba"
"git_tag" : "v0.7.2-13-g60df288"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3320,7 +3317,7 @@ workflow run_wf {
// Remove the trailing '_'
def lane_remove_trailing = lane == null ? "" : lane.replaceAll('_$', "")
def sample_id = parsedFastq[0][1]
if (sample_id in state.ignore) {
if (sample_id in ["Undetermined"] || (state.pools && !state.pools.isEmpty() && !state.pools.contains(sample_id))) {
return null
}
return [

9
target/nextflow/utils/listInputDir/nextflow_schema.json
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@@ -16,16 +16,13 @@
"description": "Path to the directory containing fastq files",
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"fastq_dir\"`. "
},
"ignore": {
"pools": {
"type": "array",
"items": {
"type": "string"
},
"description": "Pool names to ignore.",
"help_text": "Type: `string`, multiple: `True`, default: `[\"Undetermined\"]`. ",
"default": [
"Undetermined"
]
"description": "Pool names to include",
"help_text": "Type: `string`, multiple: `True`. "
},
"r1_output": {
"type": "string",

4
target/nextflow/utils/save_params/.config.vsh.yaml
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@@ -151,9 +151,9 @@ build_info:
output: "target/nextflow/utils/save_params"
executable: "target/nextflow/utils/save_params/main.nf"
viash_version: "0.9.4"
git_commit: "5a046ba00351f55ce8e9f524bc329dabda0a7a14"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-12-g5a046ba"
git_tag: "v0.7.2-13-g60df288"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/utils/save_params/main.nf
View File

@@ -3223,9 +3223,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/utils/save_params",
"viash_version" : "0.9.4",
"git_commit" : "5a046ba00351f55ce8e9f524bc329dabda0a7a14",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-12-g5a046ba"
"git_tag" : "v0.7.2-13-g60df288"
},
"package_config" : {
"name" : "htrnaseq",