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Build branch main with version main (1e04724)

Browse Source 
Build pipeline: viash-hub.htrnaseq.main-qcd6f

Source commit: 1e04724002

Source message: Integration tests: check contents of demultiplexing output (#25)
This commit is contained in:
CI
2024-12-20 11:27:04 +00:00
parent 51a1df053e
commit 5196df6cd0
55 changed files with 5916 additions and 88 deletions
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41
src/integration_test_components/well_demultiplexing/check_cutatapt_output/config.vsh.yaml Normal file
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@@ -0,0 +1,41 @@
name: "check_cutadapt_output"
namespace: "integration_test_components/well_demultiplexing"
description: "This component test the cutadapt output from the well_demultiplex subworkflow."
authors:
- __merge__: /src/base/authors/dries_schaumont.yaml
roles: [ author, maintainer ]
argument_groups:
- name: Inputs
arguments:
- name: "--fastq_r1"
type: file
required: true
multiple: true
description: Path to the forward reads to test.
- name: "--fastq_r2"
type: file
required: true
multiple: true
description: Path to the reverse reads to test.
- name: "--ids"
type: string
description: "Well IDs for the corresponding fastq input"
required: true
multiple: true
resources:
- type: python_script
path: script.py
engines:
- type: docker
image: python:3.12-slim
setup:
- type: apt
packages:
- procps
- type: python
packages:
- dnaio
runners:
- type: executable
- type: nextflow

75
src/integration_test_components/well_demultiplexing/check_cutatapt_output/script.py Normal file
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@@ -0,0 +1,75 @@
import dnaio
from operator import itemgetter
## VIASH START
par = {
}
## VIASH END
def assert_number_of_reads(reads):
expected_number_of_reads = {
"SRR14730301__A1": 165,
"SRR14730301__B1": 194,
"SRR14730302__A1": 141,
"SRR14730302__B1": 213
}
for input_id, expected_reads in expected_number_of_reads.items():
num_reads = len(reads[input_id])
assert num_reads == expected_reads, \
f"Expected number of ouput reads for {input_id} to be {expected_reads}, was {num_reads}."
def string_difference(string1, string2):
result = 0
for char1, char2 in zip(string1, string2, strict=True):
if char1.lower() != char2.lower():
result += 1
return result
def assert_barcodes_not_removed(reads):
barcodes = {
"SRR14730301__A1": "ACACCGAATT",
"SRR14730302__A1": "ACACCGAATT",
"SRR14730301__B1": "GGCTATTGAT",
"SRR14730302__B1": "GGCTATTGAT"
}
for sample_id, barcode in barcodes.items():
sample_reads = reads[sample_id]
forward_reads = map(itemgetter(0), sample_reads)
for i, forward_read in enumerate(forward_reads):
read_sequence = forward_read.sequence
read_barcode_start = read_sequence[: len(barcode)]
# A 10% difference is allowed.
assert string_difference(read_barcode_start, barcode) <= (0.1 * len(barcode)), \
(f"Expected barcode {barcode} to be present for sample {sample_id} "
f"in read {i}. Found {read_barcode_start}")
def create_input_mapping(sample_ids, inputs_r1, inputs_r2):
return {sample_id: [input_r1, input_r2]
for sample_id, input_r1, input_r2
in zip(sample_ids, inputs_r1, inputs_r2, strict=True)}
def read_input_files(input_mapping):
expected_keys = {"SRR14730301__A1", "SRR14730301__B1",
"SRR14730302__A1", "SRR14730302__B1"}
difference = set(input_mapping.keys()) - expected_keys
assert not difference, f"Found unexpected output id(s): {difference}"
result = {}
for input_id, input_files in input_mapping.items():
input_r1, input_r2 = input_files
# This reads the files into memory,
# but they are reasonably small
with dnaio.open(input_r1) as r1_reads, dnaio.open(input_r2) as r2_reads:
for r1_read, r2_read in zip(r1_reads, r2_reads, strict=True):
result.setdefault(input_id, []).append((r1_read, r2_read))
return result
def main(par):
inputs = create_input_mapping(par["ids"], par["fastq_r1"], par["fastq_r2"])
reads = read_input_files(inputs)
assert_number_of_reads(reads)
assert_barcodes_not_removed(reads)
if __name__ == "__main__":
main(par)

14
src/workflows/well_demultiplex/test.nf
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@@ -1,4 +1,5 @@
include { well_demultiplex } from params.rootDir + "/target/nextflow/workflows/well_demultiplex/main.nf"
include { check_cutadapt_output } from params.rootDir + "/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
params.resources_test = "gs://viash-hub-test-data/htrnaseq/v1/"
@@ -38,6 +39,19 @@ workflow test_wf {
| view { output ->
assert output.size() == 4 : "2 samples, each with 2 barcodes"
}
| map {output ->
def ids = output.collect{it[0]}
def states = output.collect{it[1]}
def new_state = [
"ids": ids,
"fastq_r1": states.collect{it.output_r1}.flatten(),
"fastq_r2": states.collect{it.output_r2}.flatten()
]
["integration_test_check", new_state]
}
| check_cutadapt_output.run(
fromState: {id, state -> state}
)
}

4
target/executable/eset/create_eset/.config.vsh.yaml
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@@ -220,8 +220,8 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -488,9 +488,9 @@ remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Seurat/Seur
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="2024-12-19T12:36:40Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:49Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -177,8 +177,8 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -478,9 +478,9 @@ 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="2024-12-19T12:36:42Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:51Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -191,8 +191,8 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -488,9 +488,9 @@ 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="2024-12-19T12:36:40Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:48Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -148,8 +148,8 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -470,9 +470,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
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="2024-12-19T12:36:42Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:50Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

192
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml Normal file
View File

@@ -0,0 +1,192 @@
name: "check_cutadapt_output"
namespace: "integration_test_components/well_demultiplexing"
version: "main"
authors:
- name: "Dries Schaumont"
roles:
- "author"
- "maintainer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--fastq_r1"
description: "Path to the forward reads to test."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--fastq_r2"
description: "Path to the reverse reads to test."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "string"
name: "--ids"
description: "Well IDs for the corresponding fastq input"
info: null
required: true
direction: "input"
multiple: true
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "This component test the cutadapt output from the well_demultiplex subworkflow."
info: null
status: "enabled"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/htrnaseq"
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"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
- type: "python"
user: false
packages:
- "dnaio"
upgrade: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/integration_test_components/well_demultiplexing/check_cutatapt_output/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
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: "0.9.0"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
info:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "high-throughput"
- "mapping"
- "counting"
- "pipeline"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/htrnaseq"
issue_tracker: "https://github.com/viash-hub/htrnaseq/issues"

1236
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output Executable file
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File diff suppressed because it is too large Load Diff

108
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow_labels.config Normal file
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@@ -0,0 +1,108 @@
executor {
$k8s {
submitRateLimit = '10sec'
pollInterval = '1 sec'
}
}
process {
container = 'nextflow/bash:latest'
// default resources
memory = { 8.Gb * task.attempt }
cpus = 8
maxForks = 36
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = 192.GB
// Resource labels
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 8 }
withLabel: midcpu { cpus = 16 }
withLabel: highcpu { cpus = 32 }
withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
}
profiles {
// detect tempdir
tempDir = java.nio.file.Paths.get(
System.getenv('NXF_TEMP') ?:
System.getenv('VIASH_TEMP') ?:
System.getenv('TEMPDIR') ?:
System.getenv('TMPDIR') ?:
'/tmp'
).toAbsolutePath()
mount_temp {
docker.temp = tempDir
podman.temp = tempDir
charliecloud.temp = tempDir
}
no_publish {
process {
withName: '.*' {
publishDir = [
enabled: false
]
}
}
}
docker {
docker.fixOwnership = true
docker.enabled = true
// docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
local {
// This config is for local processing.
process {
withName: ".*parallel_map_process" {
maxForks = 1
}
maxMemory = 25.GB
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 4 }
withLabel: midcpu { cpus = 6 }
withLabel: highcpu { cpus = 8 }
withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 12.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 20.GB * task.attempt ) } }
}
}
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}

4
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -264,8 +264,8 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/parallel_map/parallel_map
View File

@@ -517,9 +517,9 @@ 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="2024-12-19T12:36:41Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:49Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -201,8 +201,8 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -476,9 +476,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
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="2024-12-19T12:36:41Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:50Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -490,9 +490,9 @@ 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="2024-12-19T12:36:40Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:49Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

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

@@ -483,9 +483,9 @@ 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="2024-12-19T12:36:40Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:48Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -262,8 +262,8 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -520,9 +520,9 @@ 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="2024-12-19T12:36:41Z"
LABEL org.opencontainers.image.created="2024-12-20T10:03:49Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
LABEL org.opencontainers.image.revision="1e04724002db16babe7015e8703aa3eb55e8f225"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -220,8 +220,8 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/eset/create_eset/main.nf
View File

@@ -3090,8 +3090,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -177,8 +177,8 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3044,8 +3044,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -191,8 +191,8 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3058,8 +3058,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -148,8 +148,8 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -2997,8 +2997,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

192
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml Normal file
View File

@@ -0,0 +1,192 @@
name: "check_cutadapt_output"
namespace: "integration_test_components/well_demultiplexing"
version: "main"
authors:
- name: "Dries Schaumont"
roles:
- "author"
- "maintainer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--fastq_r1"
description: "Path to the forward reads to test."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--fastq_r2"
description: "Path to the reverse reads to test."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "string"
name: "--ids"
description: "Well IDs for the corresponding fastq input"
info: null
required: true
direction: "input"
multiple: true
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "This component test the cutadapt output from the well_demultiplex subworkflow."
info: null
status: "enabled"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/htrnaseq"
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"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
- type: "python"
user: false
packages:
- "dnaio"
upgrade: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/integration_test_components/well_demultiplexing/check_cutatapt_output/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
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: "0.9.0"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"
description: "High-throughput pipeline [WIP]\n"
info:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
\ dest: 'nextflow_labels.config'}\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "sequence"
- "high-throughput"
- "mapping"
- "counting"
- "pipeline"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/htrnaseq"
issue_tracker: "https://github.com/viash-hub/htrnaseq/issues"

3646
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf Normal file
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126
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config Normal file
View File

@@ -0,0 +1,126 @@
manifest {
name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'main'
description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
author = 'Dries Schaumont'
}
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 }
}
includeConfig("nextflow_labels.config")

108
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow_labels.config Normal file
View File

@@ -0,0 +1,108 @@
executor {
$k8s {
submitRateLimit = '10sec'
pollInterval = '1 sec'
}
}
process {
container = 'nextflow/bash:latest'
// default resources
memory = { 8.Gb * task.attempt }
cpus = 8
maxForks = 36
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = 192.GB
// Resource labels
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 8 }
withLabel: midcpu { cpus = 16 }
withLabel: highcpu { cpus = 32 }
withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
}
profiles {
// detect tempdir
tempDir = java.nio.file.Paths.get(
System.getenv('NXF_TEMP') ?:
System.getenv('VIASH_TEMP') ?:
System.getenv('TEMPDIR') ?:
System.getenv('TMPDIR') ?:
'/tmp'
).toAbsolutePath()
mount_temp {
docker.temp = tempDir
podman.temp = tempDir
charliecloud.temp = tempDir
}
no_publish {
process {
withName: '.*' {
publishDir = [
enabled: false
]
}
}
}
docker {
docker.fixOwnership = true
docker.enabled = true
// docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
local {
// This config is for local processing.
process {
withName: ".*parallel_map_process" {
maxForks = 1
}
maxMemory = 25.GB
withLabel: verylowcpu { cpus = 2 }
withLabel: lowcpu { cpus = 4 }
withLabel: midcpu { cpus = 6 }
withLabel: highcpu { cpus = 8 }
withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 12.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 20.GB * task.attempt ) } }
}
}
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}

90
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow_schema.json Normal file
View File

@@ -0,0 +1,90 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "check_cutadapt_output",
"description": "This component test the cutadapt output from the well_demultiplex subworkflow.",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"fastq_r1": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Path to the forward reads to test",
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Path to the forward reads to test."
}
,
"fastq_r2": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Path to the reverse reads to test",
"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Path to the reverse reads to test."
}
,
"ids": {
"type":
"string",
"description": "Type: List of `string`, required, multiple_sep: `\";\"`. Well IDs for the corresponding fastq input",
"help_text": "Type: List of `string`, required, multiple_sep: `\";\"`. Well IDs for the corresponding fastq input"
}
}
},
"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/inputs"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

4
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -264,8 +264,8 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/parallel_map/main.nf
View File

@@ -3148,8 +3148,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -201,8 +201,8 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/report/create_report/main.nf
View File

@@ -3077,8 +3077,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -198,8 +198,8 @@ build_info:
output: "target/nextflow/stats/combine_star_logs"
executable: "target/nextflow/stats/combine_star_logs/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3060,8 +3060,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ build_info:
output: "target/nextflow/stats/generate_pool_statistics"
executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3044,8 +3044,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -262,8 +262,8 @@ build_info:
output: "target/nextflow/stats/generate_well_statistics"
executable: "target/nextflow/stats/generate_well_statistics/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3135,8 +3135,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -308,8 +308,8 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/stats/combine_star_logs"
- "target/nextflow/stats/generate_pool_statistics"

4
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -3210,8 +3210,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/parallel_map_wf/.config.vsh.yaml
View File

@@ -175,8 +175,8 @@ build_info:
output: "target/nextflow/workflows/parallel_map_wf"
executable: "target/nextflow/workflows/parallel_map_wf/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/parallel_map"
- "target/nextflow/workflows/utils/groupWells"

4
target/nextflow/workflows/parallel_map_wf/main.nf
View File

@@ -3028,8 +3028,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/parallel_map_wf",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
View File

@@ -185,8 +185,8 @@ build_info:
output: "target/nextflow/workflows/utils/groupWells"
executable: "target/nextflow/workflows/utils/groupWells/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/workflows/utils/groupWells/main.nf
View File

@@ -3039,8 +3039,8 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/workflows/utils/groupWells",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
View File

@@ -255,8 +255,8 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790"
git_remote: "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
git_commit: "1e04724002db16babe7015e8703aa3eb55e8f225"
git_remote: "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"

4
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3134,8 +3134,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "e3a7de40e8c1f809e7a3e2ca1e34e2f7150d0790",
"git_remote" : "https://x-access-token:ghs_nFNHagvyTq2ZDrbyQ3KbmmqZYpur9V22CgJA@github.com/viash-hub/htrnaseq"
"git_commit" : "1e04724002db16babe7015e8703aa3eb55e8f225",
"git_remote" : "https://x-access-token:ghs_E2WtcKgkiH3ocUC9OYqZa56DfTo5Fl2Cb5ve@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",