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Build branch main with version main (d70fdf2)

Browse Source 
Build pipeline: viash-hub.htrnaseq.main-66qr4

Source commit: d70fdf2a6f

Source message: Fix processing multiple lanes. (#67)
This commit is contained in:
CI
2025-08-18 11:34:46 +00:00
parent e24f1ffc55
commit b51996294b
110 changed files with 4685 additions and 306 deletions
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9
CHANGELOG.md
View File

@@ -5,6 +5,15 @@
* `runner`: Replaced `ignore` parameter with `pools` paremeter. When set, only the selected pools are included for analysis.
By default all pools are selected (PR #66)
## Bug fixes
* Fix an error where processing FASTQ files from multiple lanes would cause an assertion error requesting the well demultiplexing
output to reside in one directory (PR #67).
# Minor changes
* `generate_well_statistics`: update base image to `python:3.13-trixie` (PR #67).
# htrnaseq v0.9.1
## Bug fixes

2
_viash.yaml
View File

@@ -45,7 +45,7 @@ viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |

12
src/stats/generate_well_statistics/config.vsh.yaml
View File

@@ -75,20 +75,10 @@ test_resources:
engines:
- type: docker
image: debian:stable-slim
image: python:3.13-trixie
setup:
- type: docker
env:
- PIP_BREAK_SYSTEM_PACKAGES=1
- HTSLIB_LIBRARY_DIR=/usr/lib/
- HTSLIB_INCLUDE_DIR=/usr/include/
- type: apt
packages:
- python3
- python3-pip
- python3-venv
- python-is-python3
- libhts-dev
- procps
- type: python
packages:

2
src/utils/listInputDir/main.nf
View File

@@ -57,7 +57,7 @@ workflow run_wf {
def new_state = fastq_state +
r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} +
["_meta": ["join_id": id]]
def new_id = lane?.trim() ? sample_id : "${sample_id}_${lane}".toString()
def new_id = lane?.trim() ? "${sample_id}_${lane}".toString() : sample_id
return [new_id, new_state]
}
return result

2
src/workflows/htrnaseq/main.nf
View File

@@ -95,7 +95,7 @@ workflow run_wf {
toState: {id, result, state ->
def all_fastq = result.output_r1 + result.output_r2
def output_dir = all_fastq.collect{it.parent}.unique()
assert output_dir.size() == 1, "Expected output from well demultiplexing to reside into one directory."
assert output_dir.size() == 1, "Expected output from well demultiplexing (id $id) to reside into one directory. Found: $output_dir"
def new_state = state + [
"input_r1": result.output_r1,
"input_r2": result.output_r2,

9
src/workflows/runner/integration_test.sh
View File

@@ -11,3 +11,12 @@ nextflow \
-entry test_wf \
-resume \
-profile docker,local
nextflow \
run . \
-main-script src/workflows/runner/test.nf \
-config ./src/config/labels.config \
-entry test_wf_with_lanes \
-resume \
-profile docker,local

1
src/workflows/runner/main.nf
View File

@@ -94,6 +94,7 @@ workflow run_wf {
]
return [id, new_state]
}
| view {"Pool inputs after listing directory: $it"}
| htrnaseq.run(
args: [
f_data: 'fData/$id.txt',

137
src/workflows/runner/test.nf
View File

@@ -102,6 +102,143 @@ workflow test_wf {
}
workflow.onComplete = {
try {
// Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
// So in order for the assert statement to work (or allow other errors to let the tests to fail)
// We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
// The error message will show up in .nextflow.log
def fastq_subdir = file("${params.fastq_publish_dir}")
assert fastq_subdir.isDirectory()
def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
def expected_run_folders = ["run_1", "run_2", "run_3"].toSet()
assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
unique_dirs = [
"run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
"run2": files("${fastq_subdir.toUriString()}/run_2/*_htrnaseq_${pipeline_version}", type: 'any'),
"run3": files("${fastq_subdir.toUriString()}/run_3/*_htrnaseq_${pipeline_version}", type: 'any'),
]
assert unique_dirs.every{it.value.size() == 1}
unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
assert unique_dirs.every{it.value.isDirectory()}
assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
def expected_samples = [
"run1": "VH02001612",
"run2": "VH02001612",
"run3": "VH02001614"
]
unique_dirs.each{_key, _value ->
def expected_sample = expected_samples[_key]
def expected_sample_dir = _value.resolve(expected_sample)
assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
def expected_fastq_files = [
"A1_R1_001.fastq", "A1_R2_001.fastq",
"B1_R1_001.fastq", "B1_R2_001.fastq",
"unknown_R1_001.fastq", "unknown_R2_001.fastq"]
def found_files = files("${expected_sample_dir}/*.fastq", type: 'any')
assert found_files.every{it.isFile()}
assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
}
def results_subdir = file("${params.results_publish_dir}")
assert fastq_subdir.isDirectory()
def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
assert expected_subdir.isDirectory()
def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
assert expected_result_dir.size() == 1
expected_result_dir = expected_result_dir[0]
assert expected_result_dir.isDirectory()
def expected_esets = ["VH02001612.rds", "VH02001614.rds"]
def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
assert found_esets.size() == 2
assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"]
def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
assert found_pdata.size() == 2
assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
assert found_nr_genes_nr_reads.size() == 2
assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet()
def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
assert found_star_logs.size() == 2
assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
def star_output = file("${expected_result_dir}/star_output", type: 'any')
assert star_output.isDirectory()
assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
assert file("${expected_result_dir}/report.html").isFile()
assert file("${expected_result_dir}/params.yaml").isFile()
assert file("${expected_result_dir}/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
} catch (Exception e) {
throw new WorkflowScriptErrorException("Integration test failed!", e)
}
}
}
workflow test_wf_with_lanes {
pipeline_version = get_version(viash_config)
resources_test = file(params.resources_test)
// results_publish_dir and results_publish_dir are inherited using params
// but they must be defined in the state as well because viash will check
// if all arguments are present in the hashmap
output_ch = Channel.fromList([
[
id: "run_1",
input: resources_test.resolve("10k_with_lanes/SRR14730301"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
],
[
id: "run_2",
input: resources_test.resolve("10k_with_lanes/SRR14730301"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
],
[
id: "run_3",
input:resources_test.resolve("10k_with_lanes/SRR14730302"),
genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
project_id: "foo",
experiment_id: "bar",
fastq_publish_dir: params.fastq_publish_dir,
results_publish_dir: params.results_publish_dir,
]
])
| map { state -> [state.id, state]}
| runner.run(
toState: { id, output, state -> output + [orig_input: state.input] }
)
| view { output ->
assert output.size() == 2 : "outputs should contain two elements; [id, file]"
"Output: $output"
}
tosortedlistch = output_ch
| toSortedList()
| map {events ->
assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
}
workflow.onComplete = {
try {
// Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).

2
src/workflows/well_demultiplex/config.vsh.yaml
View File

@@ -61,6 +61,8 @@ dependencies:
repository: bb
- name: concat_text
repository: cb
- name: move_files_to_directory
repository: cb
repositories:
- name: bb
type: vsh

61
src/workflows/well_demultiplex/main.nf
View File

@@ -11,6 +11,10 @@ workflow run_wf {
must be started multiple times and we need an event per lane. The events are
created by taking the R1 and R2 pairs from the input lists. The index of the elements
in these lists are added to the ID in order to make them unique.
The same pools may be present in multiple sequencing runs. Here, the events must be unique
across boths runs and samples. When called from the htrnaseq workflow; the events have the
format '{pool_id}/{run_id}'
*/
| flatMap {id, state ->
assert state.input_r1.size() == state.input_r2.size(), \
@@ -24,7 +28,7 @@ workflow run_wf {
def newState = state + [
"input_r1": state.input_r1[0],
"input_r2": state.input_r2[0],
"pool": id,
"pool_and_run_id": id,
"n_lanes": 1,
"lane_sorting": 1,
]
@@ -39,7 +43,7 @@ workflow run_wf {
def single_input_r2 = input_pair[1]
def newState = state + ["input_r1": single_input_r1,
"input_r2": single_input_r2,
"pool": id,
"pool_and_run_id": id,
"n_lanes": state.input_r1.size(),
"lane_sorting": index]
def newId = id + "_" + index
@@ -49,15 +53,13 @@ workflow run_wf {
| cutadapt.run(
directives: [label: ["highmem", "midcpu"]],
fromState: { id, state ->
// Remark: the fastq path part may seem superfluous but is necessary for publising later
def new_output = ("fastq/${id}/*_001.fastq")
[
input: state.input_r1,
input_r2: state.input_r2,
no_indels: true,
action: "none",
front_fasta: state.barcodesFasta,
output: new_output,
output: "*_001.fastq",
error_rate: 0.10,
demultiplex_mode: "single",
output_r1: state.output_r1,
@@ -66,7 +68,7 @@ workflow run_wf {
},
toState: { id, result, state ->
def newState = [
"pool": state.pool,
"pool_and_run_id": state.pool_and_run_id,
"n_lanes": state.n_lanes,
"output": result.output,
"lane_sorting": state.lane_sorting,
@@ -87,11 +89,11 @@ workflow run_wf {
def pair_end = path_as_string.endsWith("_R1_001.fastq") ? "R1" : "R2"
// Use the start of the file
def barcode_id = p.name - ~/_R(1|2)_001\.fastq$/
def new_id = state.pool + "__" + barcode_id
def new_id = state.pool_and_run_id + "__" + barcode_id
[
new_id,
[
"pool": state.pool,
"pool_and_run_id": state.pool_and_run_id,
"barcode_id": barcode_id,
"output": p,
"pair_end": pair_end,
@@ -140,7 +142,7 @@ workflow run_wf {
def (first, second) = pair
def should_be_the_same = [
"barcode_id",
"pool",
"pool_and_run_id",
"lane_sorting",
]
should_be_the_same.each { attr_to_check ->
@@ -194,8 +196,12 @@ workflow run_wf {
// It is the Id by which the events were joined using groupTuple
return [group_key.target, new_state]
}
| view {"State after running cutadapt: $it"}
// TODO: Expand this into matching a whitelist/blacklist of barcodes
// ... and turn into separate component
// This is contatenation of the FASTQ files from different lanes
// Concatenation of FASTQ files from the different runs is done later.
| concat_text.run(
directives: [label: ["lowmem", "lowcpu"]],
key: "concat_txt_r1",
@@ -204,10 +210,7 @@ workflow run_wf {
[
input: state.output_r1,
gzip_output: false,
// Remark: the fastq path part may seem superfluous but is necessary for publising later
// Also: match this with the specified output file names from cutadapt!
// Otherwise, the output file names will differ depending on wether concatenation is done or not
output: "fastq/${state.pool}/${state.barcode_id}_R1_001.fastq"
output: "${state.barcode_id}_R1_001.fastq"
]
},
toState: { id, result, state ->
@@ -223,10 +226,7 @@ workflow run_wf {
[
input: state.output_r2,
gzip_output: false,
// Remark: the fastq path part may seem superfluous but is necessary for publising later
// Also: match this with the specified output file names from cutadapt!
// Otherwise, the output file names will differ depending on wether concatenation is done or not
output: "fastq/${state.pool}/${state.barcode_id}_R2_001.fastq",
output: "${state.barcode_id}_R2_001.fastq",
]
},
toState: { id, result, state ->
@@ -236,16 +236,39 @@ workflow run_wf {
)
// Group the concatenated files back on pool level
| map {id, state ->
def new_event = [state.pool, state]
def new_event = [state.pool_and_run_id, state]
return new_event
}
| groupTuple(by: 0, sort: {a, b -> a.barcode_id <=> b.barcode_id})
| map {id, states ->
def output_r1 = states.collect{it.output_r1}.flatten()
def output_r2 = states.collect{it.output_r2}.flatten()
def output_state = ["output_r1": output_r1, "output_r2": output_r2]
def pools = states.collect{it.pool_and_run_id}
assert pools.toSet().size() == 1, "Unexpected state: pool ID to be unique. Found: ${pools}."
def output_state = ["output_r1": output_r1, "output_r2": output_r2, "pool_and_run_id": pools[0]]
return [id, output_state]
}
// The concatenation of lanes happens in different work directories (each well is processed a different
// concat_text process). Here we make sure that the FASTQ files are gathered in a single directory.
// This could be skipped when no concatenation was done since cutadapt will output in a directory already.
// But since we are copying symlinks most of the time there is almost no performance penalty here.
| move_files_to_directory.run(
fromState: { id, state ->
[
"input": state.output_r1 + state.output_r2,
// Remark: the fastq path part may seem superfluous but is necessary for publising later
"output": "fastq/${state.pool_and_run_id}/",
"keep_symbolic_links": true
]
},
toState: {id, result, state ->
def new_state = [
"output_r1": state.output_r1.collect{result.output.resolve(it.name)},
"output_r2": state.output_r2.collect{result.output.resolve(it.name)},
]
new_state
}
)
emit:
output_ch

187
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/.config.vsh.yaml Normal file
View File

@@ -0,0 +1,187 @@
name: "move_files_to_directory"
version: "v0.2.0"
authors:
- name: "Dorien Roosen"
roles:
- "maintainer"
info:
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Arguments"
arguments:
- type: "file"
name: "--input"
description: "Paths of the files that will be copied into the output directory."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--output"
description: "Path to output directory"
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
summary: "Publish one or multiple files to the same directory"
description: "This component copies one or multiple files to the same destination\
\ directory, creating the output directory if it doesn't exist."
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "debian:latest"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/move_files_to_directory/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
output: "target/nextflow/move_files_to_directory"
executable: "target/nextflow/move_files_to_directory/main.nf"
viash_version: "0.9.4"
git_commit: "1c1b0a4a1aff891ab678072b0ba915ac3ac71610"
git_remote: "https://github.com/viash-hub/craftbox"
git_tag: "v0.1.0-8-g1c1b0a4"
package_config:
name: "craftbox"
version: "v0.2.0"
summary: "A collection of custom-tailored scripts and applied utilities built with\
\ Viash.\n"
description: "`craftbox` is a curated collection of custom scripts and utilities\
\ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
\ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
\ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
\ Ready:** Components are built to run directly via the command line or be smoothly\
\ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
\ scripts and tools developed for particular tasks that may not be found in broader\
\ collections.\n* **High Quality Standards (promoted by Viash):**\n * Clear\
\ documentation for components and their parameters.\n * Full exposure of underlying\
\ script/tool arguments for fine-grained control.\n * Containerized (Docker)\
\ to ensure dependency management and a consistent, reproducible runtime environment.\n\
\ * Unit tested where applicable to ensure components function as expected.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
keywords:
- "scripts"
- "custom"
- "implementations"
- "utilities"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/main.nf Normal file
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126
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/nextflow.config Normal file
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@@ -0,0 +1,126 @@
manifest {
name = 'move_files_to_directory'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
description = 'This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\'t exist.'
author = 'Dorien Roosen'
}
process.container = 'nextflow/bash:latest'
// detect tempdir
tempDir = java.nio.file.Paths.get(
System.getenv('NXF_TEMP') ?:
System.getenv('VIASH_TEMP') ?:
System.getenv('TEMPDIR') ?:
System.getenv('TMPDIR') ?:
'/tmp'
).toAbsolutePath()
profiles {
no_publish {
process {
withName: '.*' {
publishDir = [
enabled: false
]
}
}
}
mount_temp {
docker.temp = tempDir
podman.temp = tempDir
charliecloud.temp = tempDir
}
docker {
docker.enabled = true
// docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
}
process{
withLabel: mem1gb { memory = 1000000000.B }
withLabel: mem2gb { memory = 2000000000.B }
withLabel: mem5gb { memory = 5000000000.B }
withLabel: mem10gb { memory = 10000000000.B }
withLabel: mem20gb { memory = 20000000000.B }
withLabel: mem50gb { memory = 50000000000.B }
withLabel: mem100gb { memory = 100000000000.B }
withLabel: mem200gb { memory = 200000000000.B }
withLabel: mem500gb { memory = 500000000000.B }
withLabel: mem1tb { memory = 1000000000000.B }
withLabel: mem2tb { memory = 2000000000000.B }
withLabel: mem5tb { memory = 5000000000000.B }
withLabel: mem10tb { memory = 10000000000000.B }
withLabel: mem20tb { memory = 20000000000000.B }
withLabel: mem50tb { memory = 50000000000000.B }
withLabel: mem100tb { memory = 100000000000000.B }
withLabel: mem200tb { memory = 200000000000000.B }
withLabel: mem500tb { memory = 500000000000000.B }
withLabel: mem1gib { memory = 1073741824.B }
withLabel: mem2gib { memory = 2147483648.B }
withLabel: mem4gib { memory = 4294967296.B }
withLabel: mem8gib { memory = 8589934592.B }
withLabel: mem16gib { memory = 17179869184.B }
withLabel: mem32gib { memory = 34359738368.B }
withLabel: mem64gib { memory = 68719476736.B }
withLabel: mem128gib { memory = 137438953472.B }
withLabel: mem256gib { memory = 274877906944.B }
withLabel: mem512gib { memory = 549755813888.B }
withLabel: mem1tib { memory = 1099511627776.B }
withLabel: mem2tib { memory = 2199023255552.B }
withLabel: mem4tib { memory = 4398046511104.B }
withLabel: mem8tib { memory = 8796093022208.B }
withLabel: mem16tib { memory = 17592186044416.B }
withLabel: mem32tib { memory = 35184372088832.B }
withLabel: mem64tib { memory = 70368744177664.B }
withLabel: mem128tib { memory = 140737488355328.B }
withLabel: mem256tib { memory = 281474976710656.B }
withLabel: mem512tib { memory = 562949953421312.B }
withLabel: cpu1 { cpus = 1 }
withLabel: cpu2 { cpus = 2 }
withLabel: cpu5 { cpus = 5 }
withLabel: cpu10 { cpus = 10 }
withLabel: cpu20 { cpus = 20 }
withLabel: cpu50 { cpus = 50 }
withLabel: cpu100 { cpus = 100 }
withLabel: cpu200 { cpus = 200 }
withLabel: cpu500 { cpus = 500 }
withLabel: cpu1000 { cpus = 1000 }
}

81
target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/move_files_to_directory/nextflow_schema.json Normal file
View File

@@ -0,0 +1,81 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "move_files_to_directory",
"description": "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\u0027t exist.",
"type": "object",
"definitions": {
"arguments" : {
"title": "Arguments",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths of the files that will be copied into the output directory",
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Paths of the files that will be copied into the output directory."
}
,
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output`. Path to output directory",
"help_text": "Type: `file`, required, default: `$id.$key.output`. Path to output directory"
,
"default":"$id.$key.output"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

6
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -206,9 +206,9 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -231,7 +231,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/eset/create_eset/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/eset/create_eset/create_eset
View File

@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
LABEL org.opencontainers.image.created="2025-08-05T13:28:55Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,9 +183,9 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -208,7 +208,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/eset/create_fdata/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/eset/create_fdata/create_fdata
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
LABEL org.opencontainers.image.created="2025-08-05T13:28:55Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:36Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,9 +197,9 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -222,7 +222,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/eset/create_pdata/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/eset/create_pdata/create_pdata
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
LABEL org.opencontainers.image.created="2025-08-05T13:28:54Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,9 +155,9 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -180,7 +180,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/integration_test_components/htrnaseq/check_eset/check_eset
View File

@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
LABEL org.opencontainers.image.created="2025-08-05T13:28:56Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:36Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,9 +164,9 @@ build_info:
output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -189,7 +189,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
View File

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
LABEL org.opencontainers.image.created="2025-08-05T13:28:55Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:36Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/io/publish_fastqs/.config.vsh.yaml
View File

@@ -139,9 +139,9 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -164,7 +164,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/io/publish_fastqs/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/io/publish_fastqs/publish_fastqs
View File

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
LABEL org.opencontainers.image.created="2025-08-05T13:28:57Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/io/publish_results/.config.vsh.yaml
View File

@@ -202,9 +202,9 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -227,7 +227,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/io/publish_results/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/io/publish_results/publish_results
View File

@@ -450,9 +450,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
LABEL org.opencontainers.image.created="2025-08-05T13:28:56Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -285,9 +285,9 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -310,7 +310,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/parallel_map/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/parallel_map/parallel_map
View File

@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
COPY STAR /usr/local/bin/$STAR_BINARY
LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
LABEL org.opencontainers.image.created="2025-08-05T13:28:56Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -215,9 +215,9 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -240,7 +240,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/report/create_report/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/report/create_report/create_report
View File

@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component report create_report"
LABEL org.opencontainers.image.created="2025-08-05T13:28:56Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,9 +204,9 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -229,7 +229,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/stats/combine_star_logs/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/stats/combine_star_logs/combine_star_logs
View File

@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-08-05T13:28:55Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,9 +188,9 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -213,7 +213,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/stats/generate_pool_statistics/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/stats/generate_pool_statistics/generate_pool_statistics
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
LABEL org.opencontainers.image.created="2025-08-05T13:28:56Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

18
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -228,23 +228,13 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "debian:stable-slim"
image: "python:3.13-trixie"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
env:
- "PIP_BREAK_SYSTEM_PACKAGES=1"
- "HTSLIB_LIBRARY_DIR=/usr/lib/"
- "HTSLIB_INCLUDE_DIR=/usr/include/"
- type: "apt"
packages:
- "python3"
- "python3-pip"
- "python3-venv"
- "python-is-python3"
- "libhts-dev"
- "procps"
interactive: false
- type: "python"
@@ -270,9 +260,9 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -295,7 +285,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/stats/generate_well_statistics/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

11
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -447,13 +447,10 @@ function ViashDockerfile {
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM debian:stable-slim
FROM python:3.13-trixie
ENTRYPOINT []
ENV PIP_BREAK_SYSTEM_PACKAGES=1
ENV HTSLIB_LIBRARY_DIR=/usr/lib/
ENV HTSLIB_INCLUDE_DIR=/usr/include/
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y python3 python3-pip python3-venv python-is-python3 libhts-dev procps && \
DEBIAN_FRONTEND=noninteractive apt-get install -y procps && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
@@ -461,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
LABEL org.opencontainers.image.created="2025-08-05T13:28:54Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:35Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/utils/save_params/.config.vsh.yaml
View File

@@ -151,9 +151,9 @@ build_info:
output: "target/executable/utils/save_params"
executable: "target/executable/utils/save_params/save_params"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -176,7 +176,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/executable/utils/save_params/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

4
target/executable/utils/save_params/save_params
View File

@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "pyyaml"
LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
LABEL org.opencontainers.image.created="2025-08-05T13:28:56Z"
LABEL org.opencontainers.image.created="2025-08-18T10:20:37Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="60df288f92681734080e2accc0978a38b2a4bee4"
LABEL org.opencontainers.image.revision="d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -206,9 +206,9 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -231,7 +231,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/eset/create_eset/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/eset/create_eset/main.nf
View File

@@ -3309,9 +3309,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3321,7 +3321,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -183,9 +183,9 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -208,7 +208,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/eset/create_fdata/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3279,9 +3279,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3291,7 +3291,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -197,9 +197,9 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -222,7 +222,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/eset/create_pdata/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3293,9 +3293,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3305,7 +3305,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -155,9 +155,9 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -180,7 +180,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -3233,9 +3233,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3245,7 +3245,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -164,9 +164,9 @@ build_info:
output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -189,7 +189,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3244,9 +3244,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3256,7 +3256,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/io/publish_fastqs/.config.vsh.yaml
View File

@@ -139,9 +139,9 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -164,7 +164,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/io/publish_fastqs/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/io/publish_fastqs/main.nf
View File

@@ -3207,9 +3207,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3219,7 +3219,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/io/publish_results/.config.vsh.yaml
View File

@@ -202,9 +202,9 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -227,7 +227,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/io/publish_results/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/io/publish_results/main.nf
View File

@@ -3277,9 +3277,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3289,7 +3289,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -285,9 +285,9 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -310,7 +310,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/parallel_map/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/parallel_map/main.nf
View File

@@ -3379,9 +3379,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3391,7 +3391,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -215,9 +215,9 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -240,7 +240,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/report/create_report/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/report/create_report/main.nf
View File

@@ -3323,9 +3323,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3335,7 +3335,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -204,9 +204,9 @@ build_info:
output: "target/nextflow/stats/combine_star_logs"
executable: "target/nextflow/stats/combine_star_logs/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -229,7 +229,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/stats/combine_star_logs/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3295,9 +3295,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3307,7 +3307,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -188,9 +188,9 @@ build_info:
output: "target/nextflow/stats/generate_pool_statistics"
executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -213,7 +213,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/stats/generate_pool_statistics/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3279,9 +3279,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3291,7 +3291,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

18
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -228,23 +228,13 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "debian:stable-slim"
image: "python:3.13-trixie"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
env:
- "PIP_BREAK_SYSTEM_PACKAGES=1"
- "HTSLIB_LIBRARY_DIR=/usr/lib/"
- "HTSLIB_INCLUDE_DIR=/usr/include/"
- type: "apt"
packages:
- "python3"
- "python3-pip"
- "python3-venv"
- "python-is-python3"
- "libhts-dev"
- "procps"
interactive: false
- type: "python"
@@ -270,9 +260,9 @@ build_info:
output: "target/nextflow/stats/generate_well_statistics"
executable: "target/nextflow/stats/generate_well_statistics/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -295,7 +285,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/stats/generate_well_statistics/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

21
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3317,27 +3317,14 @@ meta = [
{
"type" : "docker",
"id" : "docker",
"image" : "debian:stable-slim",
"image" : "python:3.13-trixie",
"target_registry" : "images.viash-hub.com",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
"type" : "docker",
"env" : [
"PIP_BREAK_SYSTEM_PACKAGES=1",
"HTSLIB_LIBRARY_DIR=/usr/lib/",
"HTSLIB_INCLUDE_DIR=/usr/include/"
]
},
{
"type" : "apt",
"packages" : [
"python3",
"python3-pip",
"python3-venv",
"python-is-python3",
"libhts-dev",
"procps"
],
"interactive" : false
@@ -3374,9 +3361,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3386,7 +3373,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -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: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
package_config:
@@ -187,7 +187,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/utils/concatRuns/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
target/nextflow/utils/concatRuns/main.nf
View File

@@ -3229,9 +3229,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3241,7 +3241,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -169,9 +169,9 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -194,7 +194,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/utils/listInputDir/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

8
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3236,9 +3236,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.4",
"git_commit" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3248,7 +3248,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]
@@ -3346,7 +3346,7 @@ workflow run_wf {
def new_state = fastq_state +
r1_state.findAll{it.key in ["sample_id", "sample", "lane"]} +
["_meta": ["join_id": id]]
def new_id = lane?.trim() ? sample_id : "${sample_id}_${lane}".toString()
def new_id = lane?.trim() ? "${sample_id}_${lane}".toString() : sample_id
return [new_id, new_state]
}
return result

6
target/nextflow/utils/save_params/.config.vsh.yaml
View File

@@ -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: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
package_config:
name: "htrnaseq"
version: "main"
@@ -176,7 +176,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/utils/save_params/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

6
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" : "60df288f92681734080e2accc0978a38b2a4bee4",
"git_commit" : "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247",
"git_remote" : "https://github.com/viash-hub/htrnaseq",
"git_tag" : "v0.7.2-13-g60df288"
"git_tag" : "v0.7.2-14-gd70fdf2"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3235,7 +3235,7 @@ meta = [
"info" : {
"test_resources" : [
{
"path" : "gs://viash-hub-resources/htrnaseq/v1",
"path" : "gs://viash-hub-resources/htrnaseq/v2",
"dest" : "resources_test"
}
]

6
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -345,9 +345,9 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.4"
git_commit: "60df288f92681734080e2accc0978a38b2a4bee4"
git_commit: "d70fdf2a6f13819db25bfe0ac9ddb14d0aa5c247"
git_remote: "https://github.com/viash-hub/htrnaseq"
git_tag: "v0.7.2-13-g60df288"
git_tag: "v0.7.2-14-gd70fdf2"
dependencies:
- "target/nextflow/stats/combine_star_logs"
- "target/nextflow/stats/generate_pool_statistics"
@@ -383,7 +383,7 @@ package_config:
\ first.\n"
info:
test_resources:
- path: "gs://viash-hub-resources/htrnaseq/v1"
- path: "gs://viash-hub-resources/htrnaseq/v2"
dest: "resources_test"
viash_version: "0.9.4"
source: "src"

2
target/nextflow/workflows/htrnaseq/_viash.yaml
View File

@@ -10,7 +10,7 @@ links:
viash_version: 0.9.4
info:
test_resources:
- path: gs://viash-hub-resources/htrnaseq/v1
- path: gs://viash-hub-resources/htrnaseq/v2
dest: resources_test
config_mods: |
.requirements.commands := ['ps']

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