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Build branch multiple_fixes with version multiple_fixes (de0a353)

Browse Source 
Build pipeline: viash-hub.rnaseq.multiple-fixes-w4z5x

Source commit: de0a35359a

Source message: fix dependency
This commit is contained in:
CI
2024-09-23 14:44:57 +00:00
parent 38421a767c
commit 29c8cdb0a2
199 changed files with 726 additions and 17616 deletions
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38
target/nextflow/workflows/pre_processing/.config.vsh.yaml
View File

@@ -510,6 +510,40 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_json"
description: "The fastp json format report file name"
info: null
default:
- "$id.fastp_out.json"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_html"
description: "The fastp html format report file name"
info: null
default:
- "$id.fastp_out.html"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--merged_out"
description: "File name to store merged fastp output."
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "nextflow_script"
path: "main.nf"
@@ -639,8 +673,8 @@ build_info:
output: "target/nextflow/workflows/pre_processing"
executable: "target/nextflow/workflows/pre_processing/main.nf"
viash_version: "0.9.0"
git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b"
git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

43
target/nextflow/workflows/pre_processing/main.nf
View File

@@ -3406,6 +3406,45 @@ meta = [
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--trim_json",
"description" : "The fastp json format report file name",
"default" : [
"$id.fastp_out.json"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--trim_html",
"description" : "The fastp html format report file name",
"default" : [
"$id.fastp_out.html"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--merged_out",
"description" : "File name to store merged fastp output.",
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
}
]
}
@@ -3587,8 +3626,8 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing",
"viash_version" : "0.9.0",
"git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b",
"git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq"
"git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5",
"git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
},
"package_config" : {
"version" : "multiple_fixes",

33
target/nextflow/workflows/pre_processing/nextflow_schema.json
View File

@@ -584,6 +584,39 @@
}
,
"trim_json": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.trim_json.json`. The fastp json format report file name",
"help_text": "Type: `file`, default: `$id.$key.trim_json.json`. The fastp json format report file name"
,
"default": "$id.$key.trim_json.json"
}
,
"trim_html": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.trim_html.html`. The fastp html format report file name",
"help_text": "Type: `file`, default: `$id.$key.trim_html.html`. The fastp html format report file name"
,
"default": "$id.$key.trim_html.html"
}
,
"merged_out": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.merged_out.merged_out`. File name to store merged fastp output",
"help_text": "Type: `file`, default: `$id.$key.merged_out.merged_out`. File name to store merged fastp output."
,
"default": "$id.$key.merged_out.merged_out"
}
}
},