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Build branch main with version main (861319f)

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Build pipeline: vsh-ci-template-8vdc6

Source commit: 861319f5dd

Source message: Merge pull request #4 from viash-hub/update-star-align-params

update param
This commit is contained in:
CI
2025-02-03 16:59:21 +00:00
parent edccce830a
commit 5b1018434e
34 changed files with 5633 additions and 5991 deletions
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30
target/nextflow/mapping_and_qc/.config.vsh.yaml
View File

@@ -59,37 +59,32 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
- name: "pear"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "main"
- name: "falco"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "main"
- name: "multiqc"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "main"
- name: "star/star_align_reads"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "main"
- name: "samtools/samtools_stats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "main"
repositories:
- type: "vsh"
name: "bb"
repo: "vsh/biobox"
tag: "v0.1"
tag: "main"
license: "MIT"
links:
repository: "https://github.com/viash-hub/playground"
@@ -167,15 +162,14 @@ build_info:
output: "target/nextflow/mapping_and_qc"
executable: "target/nextflow/mapping_and_qc/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "ec3c23e349a796e57e6634e140325afde4515bbf"
git_commit: "861319f5ddc22d51899493bcd30e7066c42193cb"
git_remote: "https://github.com/viash-hub/playground"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/cutadapt"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/pear"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/falco"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/cutadapt"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/falco"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
package_config:
name: "playground"
version: "main"

71
target/nextflow/mapping_and_qc/main.nf
View File

@@ -2856,15 +2856,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.1"
}
},
{
"name" : "pear",
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.1"
"tag" : "main"
}
},
{
@@ -2872,7 +2864,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.1"
"tag" : "main"
}
},
{
@@ -2880,7 +2872,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.1"
"tag" : "main"
}
},
{
@@ -2888,7 +2880,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.1"
"tag" : "main"
}
},
{
@@ -2896,7 +2888,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.1"
"tag" : "main"
}
}
],
@@ -2905,7 +2897,7 @@ meta = [
"type" : "vsh",
"name" : "bb",
"repo" : "vsh/biobox",
"tag" : "v0.1"
"tag" : "main"
}
],
"license" : "MIT",
@@ -2997,7 +2989,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/mapping_and_qc",
"viash_version" : "0.9.0-RC6",
"git_commit" : "ec3c23e349a796e57e6634e140325afde4515bbf",
"git_commit" : "861319f5ddc22d51899493bcd30e7066c42193cb",
"git_remote" : "https://github.com/viash-hub/playground"
},
"package_config" : {
@@ -3033,12 +3025,11 @@ meta = [
// resolve dependencies dependencies (if any)
meta["root_dir"] = getRootDir()
include { cutadapt } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1/nextflow/cutadapt/main.nf"
include { pear } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1/nextflow/pear/main.nf"
include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1/nextflow/falco/main.nf"
include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc/main.nf"
include { star_align_reads } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1/nextflow/star/star_align_reads/main.nf"
include { samtools_stats } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats/main.nf"
include { cutadapt } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/cutadapt/main.nf"
include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/falco/main.nf"
include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf"
include { star_align_reads } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf"
include { samtools_stats } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
// inner workflow
// user-provided Nextflow code
@@ -3061,14 +3052,18 @@ workflow run_wf {
},
toState: [
"output_falco": "outdir",
]
],
directives: [label: ["lowmem", "lowcpu"]]
)
| niceView()
| cutadapt.run(
fromState: {id, state ->
[
"input": state.input_r1,
"input_r2": state.input_r2,
"quality_cutoff": "20", // Could make this a parameter
"quality_cutoff": "30", // Could make this a parameter
"quality_cutoff_r2": "30", // Could make this a parameter
"minimum_length": "60:60", // Could make this a parameter
"adapter": "CTGTCTCTTATACACATCT", // Could make this a parameter
"adapter_r2": "CTGTCTCTTATACACATCT", // Could make this a parameter
"output": "*.fastq",
@@ -3078,29 +3073,23 @@ workflow run_wf {
def newKeys = [
"trimmed_r1": output_state["output"][0],
"trimmed_r2": output_state["output"][1],
"output_cutadapt": output_state["output"]
]
def new_state = state + newKeys
return new_state
}
)
| pear.run(
fromState: [
"forward_fastq": "trimmed_r1",
"reverse_fastq": "trimmed_r2",
],
toState: [
"output_pear": "assembled",
]
},
directives: [label: ["midmem", "midmem"]]
)
| star_align_reads.run(
fromState: [
"input": "output_pear",
"genomeDir": "reference",
"input": "trimmed_r1",
"input_r2": "trimmed_r2",
"genome_dir": "reference",
],
toState: [
"output_star": "aligned_reads",
]
],
directives: [label: ["highmem", "midcpu"]]
)
| samtools_stats.run(
fromState: [
@@ -3108,7 +3097,9 @@ workflow run_wf {
],
toState: [
"output_samtools_stats": "output",
]
],
directives: [label: ["midmem", "lowcpu"]]
)
| toSortedList()
| map { events ->
@@ -3125,7 +3116,9 @@ workflow run_wf {
],
toState: [
"multiqc_output": "output_report",
]
],
directives: [label: ["midmem", "lowcpu"]]
)
| setState(["multiqc_output", "_meta"])

2
target/nextflow/mapping_and_qc/nextflow_schema.json
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@@ -60,7 +60,7 @@
"description": "Type: `file`, required, default: `$id.$key.multiqc_output.html`, example: `multiqc.html`. ",
"help_text": "Type: `file`, required, default: `$id.$key.multiqc_output.html`, example: `multiqc.html`. "
,
"default": "$id.$key.multiqc_output.html"
"default":"$id.$key.multiqc_output.html"
}