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Build branch v0.3 with version v0.3.8 (dafe2d8)

Browse Source 
Build pipeline: viash-hub.demultiplex.v0.3-brf8v

Source commit: dafe2d8290

Source message: Bump version to v0.3.8
This commit is contained in:
CI
2025-03-27 16:16:22 +00:00
parent e9dce89f32
commit cd1815354d
30 changed files with 191 additions and 133 deletions
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6
CHANGELOG.md
View File

@@ -1,3 +1,9 @@
# demultiplex v0.3.8
## Bug fixes
* Provide a proper error when a FASTQ file is empty after demultiplexing (PR #40).
# demultiplex v0.3.7
## Minor updates

2
_viash.yaml
View File

@@ -1,5 +1,5 @@
name: demultiplex
version: v0.3.7
version: v0.3.8
description: |
Demultiplexing pipeline
license: MIT

26
src/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -1,3 +1,26 @@
import java.util.zip.GZIPInputStream
import java.nio.file.Files
import java.io.BufferedInputStream
def is_empty(file_to_check){
/*
Checks if a file has content
*/
if (file_to_check.size() == 0) {
return true
}
def input_stream = Files.newInputStream(file_to_check)
def gzInputStream
try {
gzInputStream = new GZIPInputStream(new BufferedInputStream(input_stream))
} catch (java.io.EOFException ex) {
// This is not a gzipfile...
return false
}
def read_one_byte = gzInputStream.read()
return read_one_byte == -1
}
workflow run_wf {
take:
input_ch
@@ -78,6 +101,9 @@ workflow run_wf {
"Found forward: ${forward_fastq} and reverse: ${reverse_fastq}."
println "Found ${forward_fastq.size()} forward and ${reverse_fastq.size()} reverse " +
"fastq files for sample ${sample_id}"
assert forward_fastq.every{!is_empty(it)} && reverse_fastq.every{!is_empty(it)}:
"A fastq file for sample '${sample_id}' appears to be empty!"
def fastqs_state = [
"fastq_forward": forward_fastq,
"fastq_reverse": reverse_fastq,

12
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "interop_summary_to_csv"
namespace: "io"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -121,7 +121,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.7"
target_tag: "v0.3.8"
namespace_separator: "/"
setup:
- type: "apt"
@@ -146,12 +146,12 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -167,7 +167,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

14
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# interop_summary_to_csv v0.3.7
# interop_summary_to_csv v0.3.8
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "interop_summary_to_csv v0.3.7"
echo "interop_summary_to_csv v0.3.8"
echo ""
echo "Input arguments:"
echo " --input"
@@ -470,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2025-03-20T20:32:33Z"
LABEL org.opencontainers.image.created="2025-03-27T16:00:55Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
LABEL org.opencontainers.image.version="v0.3.7"
LABEL org.opencontainers.image.revision="dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
LABEL org.opencontainers.image.version="v0.3.8"
VIASHDOCKER
fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "interop_summary_to_csv v0.3.7"
echo "interop_summary_to_csv v0.3.8"
exit
;;
--input)
@@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.7'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.8'
fi
# print dockerfile

12
target/executable/io/publish/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish"
namespace: "io"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -178,7 +178,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.7"
target_tag: "v0.3.8"
namespace_separator: "/"
setup:
- type: "apt"
@@ -196,12 +196,12 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -217,7 +217,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

14
target/executable/io/publish/publish
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# publish v0.3.7
# publish v0.3.8
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "publish v0.3.7"
echo "publish v0.3.8"
echo ""
echo "Publish the processed results of the run"
echo ""
@@ -490,10 +490,10 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish"
LABEL org.opencontainers.image.created="2025-03-20T20:32:33Z"
LABEL org.opencontainers.image.created="2025-03-27T16:00:54Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
LABEL org.opencontainers.image.version="v0.3.7"
LABEL org.opencontainers.image.revision="dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
LABEL org.opencontainers.image.version="v0.3.8"
VIASHDOCKER
fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "publish v0.3.7"
echo "publish v0.3.8"
exit
;;
--input)
@@ -814,7 +814,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.7'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.8'
fi
# print dockerfile

12
target/executable/io/untar/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "untar"
namespace: "io"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -135,7 +135,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.7"
target_tag: "v0.3.8"
namespace_separator: "/"
setup:
- type: "apt"
@@ -153,12 +153,12 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -174,7 +174,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

14
target/executable/io/untar/untar
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# untar v0.3.7
# untar v0.3.8
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "untar v0.3.7"
echo "untar v0.3.8"
echo ""
echo "Unpack a .tar file. When the contents of the .tar file is just a single"
echo "directory,"
@@ -476,10 +476,10 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io untar"
LABEL org.opencontainers.image.created="2025-03-20T20:32:32Z"
LABEL org.opencontainers.image.created="2025-03-27T16:00:54Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
LABEL org.opencontainers.image.version="v0.3.7"
LABEL org.opencontainers.image.revision="dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
LABEL org.opencontainers.image.version="v0.3.8"
VIASHDOCKER
fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "untar v0.3.7"
echo "untar v0.3.8"
exit
;;
--input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.7'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.8'
fi
# print dockerfile

10
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "combine_samples"
namespace: "dataflow"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -162,12 +162,12 @@ build_info:
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -183,7 +183,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

12
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -1,4 +1,4 @@
// combine_samples v0.3.7
// combine_samples v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "combine_samples",
"namespace" : "dataflow",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3000,13 +3000,13 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -3023,7 +3023,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",

2
target/nextflow/dataflow/combine_samples/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'dataflow/combine_samples'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
}

10
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "gather_fastqs_and_validate"
namespace: "dataflow"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -138,12 +138,12 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -159,7 +159,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

38
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -1,4 +1,4 @@
// gather_fastqs_and_validate v0.3.7
// gather_fastqs_and_validate v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "gather_fastqs_and_validate",
"namespace" : "dataflow",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -2973,13 +2973,13 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -2996,7 +2996,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",
@@ -3019,6 +3019,29 @@ meta = [
// inner workflow
// user-provided Nextflow code
import java.util.zip.GZIPInputStream
import java.nio.file.Files
import java.io.BufferedInputStream
def is_empty(file_to_check){
/*
Checks if a file has content
*/
if (file_to_check.size() == 0) {
return true
}
def input_stream = Files.newInputStream(file_to_check)
def gzInputStream
try {
gzInputStream = new GZIPInputStream(new BufferedInputStream(input_stream))
} catch (java.io.EOFException ex) {
// This is not a gzipfile...
return false
}
def read_one_byte = gzInputStream.read()
return read_one_byte == -1
}
workflow run_wf {
take:
input_ch
@@ -3099,6 +3122,9 @@ workflow run_wf {
"Found forward: ${forward_fastq} and reverse: ${reverse_fastq}."
println "Found ${forward_fastq.size()} forward and ${reverse_fastq.size()} reverse " +
"fastq files for sample ${sample_id}"
assert forward_fastq.every{!is_empty(it)} && reverse_fastq.every{!is_empty(it)}:
"A fastq file for sample '${sample_id}' appears to be empty!"
def fastqs_state = [
"fastq_forward": forward_fastq,
"fastq_reverse": reverse_fastq,

2
target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'dataflow/gather_fastqs_and_validate'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
}

10
target/nextflow/demultiplex/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -244,9 +244,9 @@ build_info:
output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
dependencies:
- "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -258,7 +258,7 @@ build_info:
- "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -274,7 +274,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

12
target/nextflow/demultiplex/main.nf
View File

@@ -1,4 +1,4 @@
// demultiplex v0.3.7
// demultiplex v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3120,13 +3120,13 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -3143,7 +3143,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",

2
target/nextflow/demultiplex/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'demultiplex'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
description = 'Demultiplexing of raw sequencing data'
}

12
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "interop_summary_to_csv"
namespace: "io"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -121,7 +121,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.7"
target_tag: "v0.3.8"
namespace_separator: "/"
setup:
- type: "apt"
@@ -146,12 +146,12 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -167,7 +167,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

16
target/nextflow/io/interop_summary_to_csv/main.nf
View File

@@ -1,4 +1,4 @@
// interop_summary_to_csv v0.3.7
// interop_summary_to_csv v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "interop_summary_to_csv",
"namespace" : "io",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -2955,7 +2955,7 @@ meta = [
"id" : "docker",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.3.7",
"target_tag" : "v0.3.8",
"namespace_separator" : "/",
"setup" : [
{
@@ -2985,13 +2985,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -3008,7 +3008,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",
@@ -3431,7 +3431,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/demultiplex/io/interop_summary_to_csv",
"tag" : "v0.3.7"
"tag" : "v0.3.8"
},
"tag" : "$id"
}'''),

2
target/nextflow/io/interop_summary_to_csv/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'io/interop_summary_to_csv'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
}
process.container = 'nextflow/bash:latest'

12
target/nextflow/io/publish/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "publish"
namespace: "io"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -178,7 +178,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.7"
target_tag: "v0.3.8"
namespace_separator: "/"
setup:
- type: "apt"
@@ -196,12 +196,12 @@ build_info:
output: "target/nextflow/io/publish"
executable: "target/nextflow/io/publish/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -217,7 +217,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

16
target/nextflow/io/publish/main.nf
View File

@@ -1,4 +1,4 @@
// publish v0.3.7
// publish v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "publish",
"namespace" : "io",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3021,7 +3021,7 @@ meta = [
"id" : "docker",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.3.7",
"target_tag" : "v0.3.8",
"namespace_separator" : "/",
"setup" : [
{
@@ -3044,13 +3044,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -3067,7 +3067,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",
@@ -3518,7 +3518,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/demultiplex/io/publish",
"tag" : "v0.3.7"
"tag" : "v0.3.8"
},
"tag" : "$id"
}'''),

2
target/nextflow/io/publish/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'io/publish'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
description = 'Publish the processed results of the run'
}

12
target/nextflow/io/untar/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "untar"
namespace: "io"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -135,7 +135,7 @@ engines:
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.3.7"
target_tag: "v0.3.8"
namespace_separator: "/"
setup:
- type: "apt"
@@ -153,12 +153,12 @@ build_info:
output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -174,7 +174,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

16
target/nextflow/io/untar/main.nf
View File

@@ -1,4 +1,4 @@
// untar v0.3.7
// untar v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "untar",
"namespace" : "io",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -2974,7 +2974,7 @@ meta = [
"id" : "docker",
"image" : "debian:stable-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.3.7",
"target_tag" : "v0.3.8",
"namespace_separator" : "/",
"setup" : [
{
@@ -2997,13 +2997,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/untar",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -3020,7 +3020,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",
@@ -3473,7 +3473,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/demultiplex/io/untar",
"tag" : "v0.3.7"
"tag" : "v0.3.8"
},
"tag" : "$id"
}'''),

2
target/nextflow/io/untar/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'io/untar'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
}

10
target/nextflow/runner/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "runner"
version: "v0.3.7"
version: "v0.3.8"
argument_groups:
- name: "Input arguments"
arguments:
@@ -192,15 +192,15 @@ build_info:
output: "target/nextflow/runner"
executable: "target/nextflow/runner/main.nf"
viash_version: "0.9.0"
git_commit: "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332"
git_commit: "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.3.5-6-ge177226"
git_tag: "v0.3.5-9-gdafe2d8"
dependencies:
- "target/nextflow/demultiplex"
- "target/nextflow/io/publish"
package_config:
name: "demultiplex"
version: "v0.3.7"
version: "v0.3.8"
description: "Demultiplexing pipeline\n"
info:
test_resources:
@@ -216,7 +216,7 @@ package_config:
)'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.7'"
- ".engines[.type == 'docker'].target_tag := 'v0.3.8'"
keywords:
- "bioinformatics"
- "sequence"

12
target/nextflow/runner/main.nf
View File

@@ -1,4 +1,4 @@
// runner v0.3.7
// runner v0.3.8
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2805,7 +2805,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "runner",
"version" : "v0.3.7",
"version" : "v0.3.8",
"argument_groups" : [
{
"name" : "Input arguments",
@@ -3040,13 +3040,13 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/runner",
"viash_version" : "0.9.0",
"git_commit" : "e177226c52ca1dd5a5cf9bb0bfc108812e2aa332",
"git_commit" : "dafe2d829079bd5a9f5eb4e7cf63e92edbf1a742",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.3.5-6-ge177226"
"git_tag" : "v0.3.5-9-gdafe2d8"
},
"package_config" : {
"name" : "demultiplex",
"version" : "v0.3.7",
"version" : "v0.3.8",
"description" : "Demultiplexing pipeline\n",
"info" : {
"test_resources" : [
@@ -3063,7 +3063,7 @@ meta = [
".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.3.7'"
".engines[.type == 'docker'].target_tag := 'v0.3.8'"
],
"keywords" : [
"bioinformatics",

2
target/nextflow/runner/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'runner'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.3.7'
version = 'v0.3.8'
description = 'Runner for demultiplexing of raw sequencing data'
}