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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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20
target/nextflow/workflows/runner/.config.vsh.yaml
View File

@@ -6,7 +6,13 @@ argument_groups:
arguments:
- type: "file"
name: "--input"
description: "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`"
description: "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`.\n\
Must contains FASTQ files in the format `PoolName_S*_L*_R1_001.fastq.gz` where\n\
\ * PoolName is a unique ID for the microwell plates or combination thereof.\n\
\ * S followed by a running number: the sample number based on the order\n\
\ that samples are listed in the sample sheet (that was used to demultiplex\
\ the pools)\n starting with 1 (e.g. S1)\n * (Optional) the lane number\
\ (e.g. L001)\n * _001 fixed suffix.\n"
info: null
must_exist: true
create_parent: true
@@ -42,11 +48,11 @@ argument_groups:
multiple: false
multiple_sep: ";"
- type: "string"
name: "--ignore"
description: "Pool names to ignore."
name: "--pools"
description: "Filter the FASTQ files in the input directory to only include pools\
\ from the provided list.\nPool names are inferred from the FASTQ file names\
\ (see input argument for more information).\nBy default all pools are included.\n"
info: null
default:
- "Undetermined"
required: false
direction: "input"
multiple: true
@@ -235,9 +241,9 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/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/nextflow/utils/listInputDir"
- "target/nextflow/workflows/htrnaseq"

15
target/nextflow/workflows/runner/main.nf
View File

@@ -3040,7 +3040,7 @@ meta = [
{
"type" : "file",
"name" : "--input",
"description" : "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`",
"description" : "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`.\nMust contains FASTQ files in the format `PoolName_S*_L*_R1_001.fastq.gz` where\n * PoolName is a unique ID for the microwell plates or combination thereof.\n * S followed by a running number: the sample number based on the order\n that samples are listed in the sample sheet (that was used to demultiplex the pools)\n starting with 1 (e.g. S1)\n * (Optional) the lane number (e.g. L001)\n * _001 fixed suffix.\n",
"must_exist" : true,
"create_parent" : true,
"required" : true,
@@ -3080,11 +3080,8 @@ meta = [
},
{
"type" : "string",
"name" : "--ignore",
"description" : "Pool names to ignore.",
"default" : [
"Undetermined"
],
"name" : "--pools",
"description" : "Filter the FASTQ files in the input directory to only include pools from the provided list.\nPool names are inferred from the FASTQ file names (see input argument for more information).\nBy default all pools are included.\n",
"required" : false,
"direction" : "input",
"multiple" : true,
@@ -3333,9 +3330,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"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",
@@ -3454,7 +3451,7 @@ workflow run_wf {
| listInputDir.run(
fromState: [
"input": "input",
"ignore": "ignore",
"pools": "pools",
],
toState: { id, state, result ->
def clean_state = state.findAll{ it.key != "input" }

11
target/nextflow/workflows/runner/nextflow_schema.json
View File

@@ -13,7 +13,7 @@
"type": "string",
"format": "path",
"exists": true,
"description": "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`",
"description": "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`.\nMust contains FASTQ files in the format `PoolName_S*_L*_R1_001.fastq.gz` where\n * PoolName is a unique ID for the microwell plates or combination thereof.\n * S followed by a running number: the sample number based on the order\n that samples are listed in the sample sheet (that was used to demultiplex the pools)\n starting with 1 (e.g",
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
},
"barcodesFasta": {
@@ -37,16 +37,13 @@
"description": "",
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
},
"ignore": {
"pools": {
"type": "array",
"items": {
"type": "string"
},
"description": "Pool names to ignore.",
"help_text": "Type: `string`, multiple: `True`, default: `[\"Undetermined\"]`. ",
"default": [
"Undetermined"
]
"description": "Filter the FASTQ files in the input directory to only include pools from the provided list.\nPool names are inferred from the FASTQ file names (see input argument for more information).\nBy default all pools are included.\n",
"help_text": "Type: `string`, multiple: `True`. "
},
"umi_length": {
"type": "integer",