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Build branch prepare_reads with version prepare_reads (2bd8e1b)

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Build pipeline: viash-hub.rnaseq.prepare-reads-9nvqs

Source commit: 2bd8e1becf

Source message: update mermaid
This commit is contained in:
CI
2025-06-13 09:16:18 +00:00
parent 5ca52f50c6
commit 9ecdb612f6
10 changed files with 179 additions and 52 deletions
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28
README.md
View File

@@ -121,23 +121,29 @@ flowchart TB
flowchart TB
subgraph inputs[Inputs]
input_r1[Input R1 FastQ]
input_r2[Input R2 FastQ]
sample_metadata[Sample metadata]
input_r1[R1 reads]
input_r2[R2 reads]
input_strandedness[Strandedness]
end
input_r1 --> cat_fastq_r1 --> trim_r1 --> infer_strandedness_r1 --> processed_r1
input_r2 --> cat_fastq_r2 --> trim_r2 --> infer_strandedness_r2 --> processed_r2
input_r1 --> concat_text_r1[/concat_text/]:::comp
input_r2 --> concat_text_r2[/concat_text/]:::comp
concat_text_r1 & concat_text_r2 --> lint_fastq1[/lint_fastq/]:::comp --> trim_reads[/trim_reads/]:::comp --> lint_fastq2[/lint_fastq/]:::comp --> remove_genome_contaminants[/remove_genome_contaminants/]:::comp --> lint_fastq3[/lint_fastq/]:::comp --> remove_rRNA[/remove_rRNA/]:::comp --> lint_fastq4[/lint_fastq/]:::comp --> infer_strandedness[/infer_strandedness/]:::comp --> processed_r1 & processed_r2 & output_strandedness
processed_r1 & processed_r2 --> fastqc --> prepare_reads_qc_data
input_strandedness --> infer_strandedness
concat_text_r1 & concat_text_r2 --> fastqc_raw[/fastqc_raw/]:::comp --> fastqc_raw_multiqc
trim_reads --> fastqc_trimmed[/fastqc_trimmed/]:::comp --> fastqc_trimmed_multiqc
infer_strandedness --> strandedness_multiqc
fastqc_raw_multiqc & fastqc_trimmed_multiqc & strandedness_multiqc --> prepare_reads_multiqc
sample_metadata --> processed_metadata
subgraph outputs[Outputs]
processed_r1
processed_r2
processed_metadata
prepare_reads_qc_data
processed_r1[R1 reads]
processed_r2[R2 reads]
output_strandedness[Strandedness]
prepare_reads_multiqc[MultiQC files]
end
classDef info stroke-dasharray: 4 4

28
README.qmd
View File

@@ -127,23 +127,29 @@ flowchart TB
flowchart TB
subgraph inputs[Inputs]
input_r1[Input R1 FastQ]
input_r2[Input R2 FastQ]
sample_metadata[Sample metadata]
input_r1[R1 reads]
input_r2[R2 reads]
input_strandedness[Strandedness]
end
input_r1 --> cat_fastq_r1 --> trim_r1 --> infer_strandedness_r1 --> processed_r1
input_r2 --> cat_fastq_r2 --> trim_r2 --> infer_strandedness_r2 --> processed_r2
input_r1 --> concat_text_r1[/concat_text/]:::comp
input_r2 --> concat_text_r2[/concat_text/]:::comp
concat_text_r1 & concat_text_r2 --> lint_fastq1[/lint_fastq/]:::comp --> trim_reads[/trim_reads/]:::comp --> lint_fastq2[/lint_fastq/]:::comp --> remove_genome_contaminants[/remove_genome_contaminants/]:::comp --> lint_fastq3[/lint_fastq/]:::comp --> remove_rRNA[/remove_rRNA/]:::comp --> lint_fastq4[/lint_fastq/]:::comp --> infer_strandedness[/infer_strandedness/]:::comp --> processed_r1 & processed_r2 & output_strandedness
processed_r1 & processed_r2 --> fastqc --> prepare_reads_qc_data
input_strandedness --> infer_strandedness
concat_text_r1 & concat_text_r2 --> fastqc_raw[/fastqc_raw/]:::comp --> fastqc_raw_multiqc
trim_reads --> fastqc_trimmed[/fastqc_trimmed/]:::comp --> fastqc_trimmed_multiqc
infer_strandedness --> strandedness_multiqc
fastqc_raw_multiqc & fastqc_trimmed_multiqc & strandedness_multiqc --> prepare_reads_multiqc
sample_metadata --> processed_metadata
subgraph outputs[Outputs]
processed_r1
processed_r2
processed_metadata
prepare_reads_qc_data
processed_r1[R1 reads]
processed_r2[R2 reads]
output_strandedness[Strandedness]
prepare_reads_multiqc[MultiQC files]
end
classDef info stroke-dasharray: 4 4

15
src/prepare_reads/config.vsh.yaml
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@@ -11,24 +11,35 @@ argument_groups:
type: file
example: "reads_R2.fastq.gz"
multiple: true
required: false
- name: --input_strandedness
type: string
example: "auto"
required: false
- name: Outputs
arguments:
- name: --output_r1
type: file
direction: output
example: "fastq.gz"
required: true
- name: --output_r2
type: file
direction: output
example: "fastq.gz"
required: false
- name: --output_strandedness
type: file
type: string
direction: output
example: strandedness.yaml
required: true
dependencies:
- name: concat_text
repository: craftbox
alias: concat_r1
- name: concat_text
repository: craftbox
alias: concat_r2
resources:
- type: nextflow_script

33
src/prepare_reads/main.nf
View File

@@ -4,7 +4,7 @@ workflow run_wf {
main:
output_ch = input_ch
| concat_text.run(
| concat_r1.run(
fromState: [
input: "input_r1"
],
@@ -13,7 +13,7 @@ workflow run_wf {
]
)
| concat_text.run(
| concat_r2.run(
fromState: [
input: "input_r2"
],
@@ -21,6 +21,35 @@ workflow run_wf {
processed_r2: "output"
]
)
// TODO: add fq linter
// TODO: run fastqc on raw reads
// TODO: add fq trimmer (trimgalore or fastp)
// TODO: run fastqc on trimmed reads
// TODO: lint again?
// TODO: remove genome contaminant reads (bbmap_bbsplit)
// TODO: lint again?
// TODO: remove ribosomal RNA reads (sortmerna)
// TODO: lint again?
// TODO: infer strandedness (if not provided)
| map { id, state ->
def newState = state + ["strandedness": "forward"]
[id, newState]
}
| setState(
[
output_r1: "processed_r1",
output_r2: "processed_r2",
output_strandedness: "strandedness"
]
)
emit:
output_ch

11
src/prepare_reads/test.sh Executable file
View File

@@ -0,0 +1,11 @@
#!/bin/bash
export NXF_VER=24.04.5
viash ns build
nextflow run . \
-main-script target/nextflow/prepare_reads/main.nf \
--input_r1 resources_test/minimal_test/input_fastq/SRR6357070_1.fastq.gz \
--input_r2 resources_test/minimal_test/input_fastq/SRR6357070_2.fastq.gz \
--publish_dir test_results/test_prepare_reads

2
target/nextflow/prepare_genome/.config.vsh.yaml
View File

@@ -161,7 +161,7 @@ build_info:
output: "target/nextflow/prepare_genome"
executable: "target/nextflow/prepare_genome/main.nf"
viash_version: "0.9.4"
git_commit: "4bc267b511202938a752ce09237d0e9808f23639"
git_commit: "2bd8e1becf04860c3cf718f765e69a1511ceb7c6"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/toolbox/v0.1.1/nextflow/bgzip"

2
target/nextflow/prepare_genome/main.nf
View File

@@ -3231,7 +3231,7 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/prepare_genome",
"viash_version" : "0.9.4",
"git_commit" : "4bc267b511202938a752ce09237d0e9808f23639",
"git_commit" : "2bd8e1becf04860c3cf718f765e69a1511ceb7c6",
"git_remote" : "https://github.com/viash-hub/rnaseq"
},
"package_config" : {

29
target/nextflow/prepare_reads/.config.vsh.yaml
View File

@@ -25,6 +25,15 @@ argument_groups:
direction: "input"
multiple: true
multiple_sep: ";"
- type: "string"
name: "--input_strandedness"
info: null
example:
- "auto"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
@@ -34,7 +43,7 @@ argument_groups:
- "fastq.gz"
must_exist: true
create_parent: true
required: false
required: true
direction: "output"
multiple: false
multiple_sep: ";"
@@ -49,14 +58,10 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
- type: "string"
name: "--output_strandedness"
info: null
example:
- "strandedness.yaml"
must_exist: true
create_parent: true
required: false
required: true
direction: "output"
multiple: false
multiple_sep: ";"
@@ -72,6 +77,13 @@ scope:
target: "public"
dependencies:
- name: "concat_text"
alias: "concat_r1"
repository:
type: "vsh"
repo: "craftbox"
tag: "v0.2.0"
- name: "concat_text"
alias: "concat_r2"
repository:
type: "vsh"
repo: "craftbox"
@@ -161,10 +173,11 @@ build_info:
output: "target/nextflow/prepare_reads"
executable: "target/nextflow/prepare_reads/main.nf"
viash_version: "0.9.4"
git_commit: "4bc267b511202938a752ce09237d0e9808f23639"
git_commit: "2bd8e1becf04860c3cf718f765e69a1511ceb7c6"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
package_config:
name: "rnaseq"
version: "prepare_reads"

72
target/nextflow/prepare_reads/main.nf
View File

@@ -3061,6 +3061,17 @@ meta = [
"direction" : "input",
"multiple" : true,
"multiple_sep" : ";"
},
{
"type" : "string",
"name" : "--input_strandedness",
"example" : [
"auto"
],
"required" : false,
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
}
]
},
@@ -3075,7 +3086,7 @@ meta = [
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"required" : true,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
@@ -3094,14 +3105,9 @@ meta = [
"multiple_sep" : ";"
},
{
"type" : "file",
"type" : "string",
"name" : "--output_strandedness",
"example" : [
"strandedness.yaml"
],
"must_exist" : true,
"create_parent" : true,
"required" : false,
"required" : true,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
@@ -3125,6 +3131,16 @@ meta = [
"dependencies" : [
{
"name" : "concat_text",
"alias" : "concat_r1",
"repository" : {
"type" : "vsh",
"repo" : "craftbox",
"tag" : "v0.2.0"
}
},
{
"name" : "concat_text",
"alias" : "concat_r2",
"repository" : {
"type" : "vsh",
"repo" : "craftbox",
@@ -3233,7 +3249,7 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/prepare_reads",
"viash_version" : "0.9.4",
"git_commit" : "4bc267b511202938a752ce09237d0e9808f23639",
"git_commit" : "2bd8e1becf04860c3cf718f765e69a1511ceb7c6",
"git_remote" : "https://github.com/viash-hub/rnaseq"
},
"package_config" : {
@@ -3282,7 +3298,10 @@ meta = [
// resolve dependencies dependencies (if any)
meta["root_dir"] = getRootDir()
include { concat_text } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf"
include { concat_text as concat_r1_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf"
concat_r1 = concat_r1_viashalias.run(key: "concat_r1")
include { concat_text as concat_r2_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text/main.nf"
concat_r2 = concat_r2_viashalias.run(key: "concat_r2")
// inner workflow
// user-provided Nextflow code
@@ -3292,7 +3311,7 @@ workflow run_wf {
main:
output_ch = input_ch
| concat_text.run(
| concat_r1.run(
fromState: [
input: "input_r1"
],
@@ -3301,7 +3320,7 @@ workflow run_wf {
]
)
| concat_text.run(
| concat_r2.run(
fromState: [
input: "input_r2"
],
@@ -3309,6 +3328,35 @@ workflow run_wf {
processed_r2: "output"
]
)
// TODO: add fq linter
// TODO: run fastqc on raw reads
// TODO: add fq trimmer (trimgalore or fastp)
// TODO: run fastqc on trimmed reads
// TODO: lint again?
// TODO: remove genome contaminant reads (bbmap_bbsplit)
// TODO: lint again?
// TODO: remove ribosomal RNA reads (sortmerna)
// TODO: lint again?
// TODO: infer strandedness (if not provided)
| map { id, state ->
def newState = state + ["strandedness": "forward"]
[id, newState]
}
| setState(
[
output_r1: "processed_r1",
output_r2: "processed_r2",
output_strandedness: "strandedness"
]
)
emit:
output_ch

11
target/nextflow/prepare_reads/nextflow_schema.json
View File

@@ -26,6 +26,11 @@
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads_R2.fastq.gz\"]`. "
},
"input_strandedness": {
"type": "string",
"description": "",
"help_text": "Type: `string`, multiple: `False`, example: `\"auto\"`. "
}
}
},
@@ -38,7 +43,7 @@
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_r1.gz\"`, direction: `output`, example: `\"fastq.gz\"`. ",
"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_r1.gz\"`, direction: `output`, example: `\"fastq.gz\"`. ",
"default": "$id.$key.output_r1.gz"
},
"output_r2": {
@@ -50,10 +55,8 @@
},
"output_strandedness": {
"type": "string",
"format": "path",
"description": "",
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_strandedness.yaml\"`, direction: `output`, example: `\"strandedness.yaml\"`. ",
"default": "$id.$key.output_strandedness.yaml"
"help_text": "Type: `string`, multiple: `False`, required. "
}
}
},