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Build branch save-params with version save-params (24e6d49)

Browse Source 
Build pipeline: viash-hub.htrnaseq.save-params-tsz2t

Source commit: 24e6d49c09

Source message: PR fixes
This commit is contained in:
CI
2025-04-03 14:07:06 +00:00
parent 8ca2889a4d
commit 16ea2ebf68
71 changed files with 201 additions and 191 deletions
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7
src/utils/save_params/config.vsh.yaml
View File

@@ -1,7 +1,7 @@
name: save_params
namespace: utils
description: |
Save parameters to a file
Save parameters to a YAML file
argument_groups:
- name: Inputs
@@ -13,7 +13,7 @@ argument_groups:
required: true
- name: "--params_yaml"
description: |
base64 encoded yaml file containing the state
base64 encoded yaml containing the state
type: string
required: true
@@ -21,9 +21,10 @@ argument_groups:
arguments:
- name: "--output"
description: |
The output file
The output YAML file
type: string
required: true
example: "output.yaml"
resources:
- type: python_script

31
src/utils/save_params/script.py
View File

@@ -15,39 +15,24 @@ class Dumper(yaml.Dumper):
return super(Dumper, self).increase_indent(flow, False)
def decode_params_yaml(encoded_yaml):
# Step 1: Decode from Base64
yaml_bytes = base64.b64decode(encoded_yaml)
# Step 2: Convert bytes to string
yaml_string = yaml_bytes.decode('utf-8')
# Step 3: Extract pattern for Java path objects
# Find pattern: !!sun.nio.fs.UnixPath /path/to/file
pattern = r'!!sun\.nio\.fs\.UnixPath\s+([^\n]+)'
# Replace with the actual path string (captured group)
yaml_string = re.sub(pattern, r'\1', yaml_string)
# Handle any remaining empty UnixPath objects
yaml_string = yaml_string.replace('!!sun.nio.fs.UnixPath {}', '""')
# Step 4: Parse YAML
yaml_data = yaml.safe_load(yaml_string)
return yaml_data
def replace_id(value, sample_id):
if isinstance(value, str):
return value.replace('$id', sample_id)
elif isinstance(value, list):
return [replace_id(item, sample_id) for item in value]
return value
# def replace_id(value, sample_id):
# if isinstance(value, str):
# return value.replace('$id', sample_id)
# elif isinstance(value, list):
# return [replace_id(item, sample_id) for item in value]
# return value
print(par['params_yaml'])
params = decode_params_yaml(par['params_yaml'])
for key, value in params.items():
params[key] = replace_id(value, par["id"])
# for key, value in params.items():
# params[key] = replace_id(value, par["id"])
with open(par["output"], 'w') as f:
yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)

5
src/workflows/htrnaseq/config.vsh.yaml
View File

@@ -88,6 +88,11 @@ argument_groups:
direction: output
required: true
default: report.$id.html
- name: "--params"
type: file
direction: output
required: true
default: params.$id.yaml
resources:
- type: nextflow_script
path: main.nf

27
src/workflows/htrnaseq/main.nf
View File

@@ -11,14 +11,6 @@ workflow run_wf {
return [id, newState]
}
// The featureData only has one requirement: the genome annotation.
// It can be generated straight away. Most of the time, there is one shared
// annotation for all of the inputs and the fData should only be calculated once.
// The state is manpulated in such a way that there is one event created per unique
// input annotation file. In turn, the featureData file can joined into the original input
// channel which allows it to be shared across events if required.
f_data_ch = input_ch
| save_params.run(
fromState: {id, state ->
// Define the function before using it
@@ -26,8 +18,10 @@ workflow run_wf {
convertPaths = { value ->
if (value instanceof java.nio.file.Path)
return value.toUriString()
else if (value instanceof Collection)
else if (value instanceof List)
return value.collect { convertPaths(it) }
else if (value instanceof Collection)
throw new UnsupportedOperationException("Collections other than Lists are not supported")
else
return value
}
@@ -42,12 +36,21 @@ workflow run_wf {
return [
"id": id,
"params_yaml": encodedYaml,
"output": "${id}_parameters.yaml"
"output": "params"
]
},
toState: ["parameters": "output"]
toState: ["params": "output"]
)
// The featureData only has one requirement: the genome annotation.
// It can be generated straight away. Most of the time, there is one shared
// annotation for all of the inputs and the fData should only be calculated once.
// The state is manpulated in such a way that there is one event created per unique
// input annotation file. In turn, the featureData file can joined into the original input
// channel which allows it to be shared across events if required.
f_data_ch = input_ch
| toSortedList()
| flatMap {ids_and_states ->
def annotation_files = ids_and_states.inject([:]){ old_state, id_and_state ->
@@ -347,7 +350,7 @@ workflow run_wf {
"f_data": "f_data",
"p_data": "p_data",
"html_report": "html_report",
"parameters": "parameters",
"params": "params",
"_meta": "_meta",
])

2
target/executable/eset/create_eset/.config.vsh.yaml
View File

@@ -203,7 +203,7 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:02Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/eset/create_fdata/.config.vsh.yaml
View File

@@ -180,7 +180,7 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:02Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -194,7 +194,7 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:03Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -152,7 +152,7 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:01Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -161,7 +161,7 @@ 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: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:03Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:26Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/io/publish_fastqs/.config.vsh.yaml
View File

@@ -136,7 +136,7 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:01Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/io/publish_results/.config.vsh.yaml
View File

@@ -190,7 +190,7 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:02Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -282,7 +282,7 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:03Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:26Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -206,7 +206,7 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -462,9 +462,9 @@ 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="2025-04-01T15:16:03Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -201,7 +201,7 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:01Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -185,7 +185,7 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-04-01T15:16:02Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

2
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -267,7 +267,7 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -461,9 +461,9 @@ 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="2025-04-01T15:16:01Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER

10
target/executable/utils/save_params/.config.vsh.yaml
View File

@@ -14,7 +14,7 @@ argument_groups:
multiple_sep: ";"
- type: "string"
name: "--params_yaml"
description: "base64 encoded yaml file containing the state\n"
description: "base64 encoded yaml containing the state\n"
info: null
required: true
direction: "input"
@@ -24,8 +24,10 @@ argument_groups:
arguments:
- type: "string"
name: "--output"
description: "The output file\n"
description: "The output YAML file\n"
info: null
example:
- "output.yaml"
required: true
direction: "input"
multiple: false
@@ -37,7 +39,7 @@ resources:
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Save parameters to a file\n"
description: "Save parameters to a YAML file\n"
info: null
status: "enabled"
scope:
@@ -144,7 +146,7 @@ build_info:
output: "target/executable/utils/save_params"
executable: "target/executable/utils/save_params/save_params"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

42
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="2025-04-01T15:16:03Z"
LABEL org.opencontainers.image.created="2025-04-03T13:19:26Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
function ViashHelp {
echo "save_params save-params"
echo ""
echo "Save parameters to a file"
echo "Save parameters to a YAML file"
echo ""
echo "Inputs:"
echo " --id"
@@ -584,12 +584,13 @@ function ViashHelp {
echo ""
echo " --params_yaml"
echo " type: string, required parameter"
echo " base64 encoded yaml file containing the state"
echo " base64 encoded yaml containing the state"
echo ""
echo "Outputs:"
echo " --output"
echo " type: string, required parameter"
echo " The output file"
echo " example: output.yaml"
echo " The output YAML file"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
@@ -1078,39 +1079,24 @@ class Dumper(yaml.Dumper):
return super(Dumper, self).increase_indent(flow, False)
def decode_params_yaml(encoded_yaml):
# Step 1: Decode from Base64
yaml_bytes = base64.b64decode(encoded_yaml)
# Step 2: Convert bytes to string
yaml_string = yaml_bytes.decode('utf-8')
# Step 3: Extract pattern for Java path objects
# Find pattern: !!sun.nio.fs.UnixPath /path/to/file
pattern = r'!!sun\\.nio\\.fs\\.UnixPath\\s+([^\\n]+)'
# Replace with the actual path string (captured group)
yaml_string = re.sub(pattern, r'\\1', yaml_string)
# Handle any remaining empty UnixPath objects
yaml_string = yaml_string.replace('!!sun.nio.fs.UnixPath {}', '""')
# Step 4: Parse YAML
yaml_data = yaml.safe_load(yaml_string)
return yaml_data
def replace_id(value, sample_id):
if isinstance(value, str):
return value.replace('\$id', sample_id)
elif isinstance(value, list):
return [replace_id(item, sample_id) for item in value]
return value
# def replace_id(value, sample_id):
# if isinstance(value, str):
# return value.replace('\$id', sample_id)
# elif isinstance(value, list):
# return [replace_id(item, sample_id) for item in value]
# return value
print(par['params_yaml'])
params = decode_params_yaml(par['params_yaml'])
for key, value in params.items():
params[key] = replace_id(value, par["id"])
# for key, value in params.items():
# params[key] = replace_id(value, par["id"])
with open(par["output"], 'w') as f:
yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)

2
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -203,7 +203,7 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/eset/create_eset/main.nf
View File

@@ -3309,7 +3309,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -180,7 +180,7 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3279,7 +3279,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -194,7 +194,7 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3293,7 +3293,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -152,7 +152,7 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -3233,7 +3233,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -161,7 +161,7 @@ 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: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3244,7 +3244,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/io/publish_fastqs/.config.vsh.yaml
View File

@@ -136,7 +136,7 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/io/publish_fastqs/main.nf
View File

@@ -3207,7 +3207,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/io/publish_results/.config.vsh.yaml
View File

@@ -190,7 +190,7 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/io/publish_results/main.nf
View File

@@ -3267,7 +3267,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -282,7 +282,7 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3379,7 +3379,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -206,7 +206,7 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/report/create_report/main.nf
View File

@@ -3314,7 +3314,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -201,7 +201,7 @@ build_info:
output: "target/nextflow/stats/combine_star_logs"
executable: "target/nextflow/stats/combine_star_logs/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3295,7 +3295,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -185,7 +185,7 @@ build_info:
output: "target/nextflow/stats/generate_pool_statistics"
executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3279,7 +3279,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -267,7 +267,7 @@ build_info:
output: "target/nextflow/stats/generate_well_statistics"
executable: "target/nextflow/stats/generate_well_statistics/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3374,7 +3374,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/utils/concatRuns/.config.vsh.yaml
View File

@@ -157,7 +157,7 @@ build_info:
output: "target/nextflow/utils/concatRuns"
executable: "target/nextflow/utils/concatRuns/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"

2
target/nextflow/utils/concatRuns/main.nf
View File

@@ -3229,7 +3229,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/concatRuns",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/utils/listInputDir/.config.vsh.yaml
View File

@@ -168,7 +168,7 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/utils/listInputDir/main.nf
View File

@@ -3239,7 +3239,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

10
target/nextflow/utils/save_params/.config.vsh.yaml
View File

@@ -14,7 +14,7 @@ argument_groups:
multiple_sep: ";"
- type: "string"
name: "--params_yaml"
description: "base64 encoded yaml file containing the state\n"
description: "base64 encoded yaml containing the state\n"
info: null
required: true
direction: "input"
@@ -24,8 +24,10 @@ argument_groups:
arguments:
- type: "string"
name: "--output"
description: "The output file\n"
description: "The output YAML file\n"
info: null
example:
- "output.yaml"
required: true
direction: "input"
multiple: false
@@ -37,7 +39,7 @@ resources:
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Save parameters to a file\n"
description: "Save parameters to a YAML file\n"
info: null
status: "enabled"
scope:
@@ -144,7 +146,7 @@ build_info:
output: "target/nextflow/utils/save_params"
executable: "target/nextflow/utils/save_params/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

42
target/nextflow/utils/save_params/main.nf
View File

@@ -3054,7 +3054,7 @@ meta = [
{
"type" : "string",
"name" : "--params_yaml",
"description" : "base64 encoded yaml file containing the state\n",
"description" : "base64 encoded yaml containing the state\n",
"required" : true,
"direction" : "input",
"multiple" : false,
@@ -3068,7 +3068,10 @@ meta = [
{
"type" : "string",
"name" : "--output",
"description" : "The output file\n",
"description" : "The output YAML file\n",
"example" : [
"output.yaml"
],
"required" : true,
"direction" : "input",
"multiple" : false,
@@ -3089,7 +3092,7 @@ meta = [
"dest" : "nextflow_labels.config"
}
],
"description" : "Save parameters to a file\n",
"description" : "Save parameters to a YAML file\n",
"status" : "enabled",
"scope" : {
"image" : "public",
@@ -3218,7 +3221,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/utils/save_params",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3311,39 +3314,24 @@ class Dumper(yaml.Dumper):
return super(Dumper, self).increase_indent(flow, False)
def decode_params_yaml(encoded_yaml):
# Step 1: Decode from Base64
yaml_bytes = base64.b64decode(encoded_yaml)
# Step 2: Convert bytes to string
yaml_string = yaml_bytes.decode('utf-8')
# Step 3: Extract pattern for Java path objects
# Find pattern: !!sun.nio.fs.UnixPath /path/to/file
pattern = r'!!sun\\\\.nio\\\\.fs\\\\.UnixPath\\\\s+([^\\\\n]+)'
# Replace with the actual path string (captured group)
yaml_string = re.sub(pattern, r'\\\\1', yaml_string)
# Handle any remaining empty UnixPath objects
yaml_string = yaml_string.replace('!!sun.nio.fs.UnixPath {}', '""')
# Step 4: Parse YAML
yaml_data = yaml.safe_load(yaml_string)
return yaml_data
def replace_id(value, sample_id):
if isinstance(value, str):
return value.replace('\\$id', sample_id)
elif isinstance(value, list):
return [replace_id(item, sample_id) for item in value]
return value
# def replace_id(value, sample_id):
# if isinstance(value, str):
# return value.replace('\\$id', sample_id)
# elif isinstance(value, list):
# return [replace_id(item, sample_id) for item in value]
# return value
print(par['params_yaml'])
params = decode_params_yaml(par['params_yaml'])
for key, value in params.items():
params[key] = replace_id(value, par["id"])
# for key, value in params.items():
# params[key] = replace_id(value, par["id"])
with open(par["output"], 'w') as f:
yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)

2
target/nextflow/utils/save_params/nextflow.config
View File

@@ -3,7 +3,7 @@ manifest {
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'save-params'
description = 'Save parameters to a file\n'
description = 'Save parameters to a YAML file\n'
}
process.container = 'nextflow/bash:latest'

10
target/nextflow/utils/save_params/nextflow_schema.json
View File

@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "save_params",
"description": "Save parameters to a file\n",
"description": "Save parameters to a YAML file\n",
"type": "object",
"definitions": {
@@ -27,8 +27,8 @@
"params_yaml": {
"type":
"string",
"description": "Type: `string`, required. base64 encoded yaml file containing the state\n",
"help_text": "Type: `string`, required. base64 encoded yaml file containing the state\n"
"description": "Type: `string`, required. base64 encoded yaml containing the state\n",
"help_text": "Type: `string`, required. base64 encoded yaml containing the state\n"
}
@@ -47,8 +47,8 @@
"output": {
"type":
"string",
"description": "Type: `string`, required. The output file\n",
"help_text": "Type: `string`, required. The output file\n"
"description": "Type: `string`, required, example: `output.yaml`. The output YAML file\n",
"help_text": "Type: `string`, required, example: `output.yaml`. The output YAML file\n"
}

13
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -183,6 +183,17 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--params"
info: null
default:
- "params.$id.yaml"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "nextflow_script"
path: "main.nf"
@@ -331,7 +342,7 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/stats/combine_star_logs"

42
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -3252,6 +3252,19 @@ meta = [
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--params",
"default" : [
"params.$id.yaml"
],
"must_exist" : true,
"create_parent" : true,
"required" : true,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
}
]
}
@@ -3471,7 +3484,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3543,14 +3556,6 @@ workflow run_wf {
return [id, newState]
}
// The featureData only has one requirement: the genome annotation.
// It can be generated straight away. Most of the time, there is one shared
// annotation for all of the inputs and the fData should only be calculated once.
// The state is manpulated in such a way that there is one event created per unique
// input annotation file. In turn, the featureData file can joined into the original input
// channel which allows it to be shared across events if required.
f_data_ch = input_ch
| save_params.run(
fromState: {id, state ->
// Define the function before using it
@@ -3558,8 +3563,10 @@ workflow run_wf {
convertPaths = { value ->
if (value instanceof java.nio.file.Path)
return value.toUriString()
else if (value instanceof Collection)
else if (value instanceof List)
return value.collect { convertPaths(it) }
else if (value instanceof Collection)
throw new UnsupportedOperationException("Collections other than Lists are not supported")
else
return value
}
@@ -3574,12 +3581,21 @@ workflow run_wf {
return [
"id": id,
"params_yaml": encodedYaml,
"output": "${id}_parameters.yaml"
"output": "params"
]
},
toState: ["parameters": "output"]
toState: ["params": "output"]
)
// The featureData only has one requirement: the genome annotation.
// It can be generated straight away. Most of the time, there is one shared
// annotation for all of the inputs and the fData should only be calculated once.
// The state is manpulated in such a way that there is one event created per unique
// input annotation file. In turn, the featureData file can joined into the original input
// channel which allows it to be shared across events if required.
f_data_ch = input_ch
| toSortedList()
| flatMap {ids_and_states ->
def annotation_files = ids_and_states.inject([:]){ old_state, id_and_state ->
@@ -3879,7 +3895,7 @@ workflow run_wf {
"f_data": "f_data",
"p_data": "p_data",
"html_report": "html_report",
"parameters": "parameters",
"params": "params",
"_meta": "_meta",
])

11
target/nextflow/workflows/htrnaseq/nextflow_schema.json
View File

@@ -182,6 +182,17 @@
}
,
"params": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.params.yaml`. ",
"help_text": "Type: `file`, required, default: `$id.$key.params.yaml`. "
,
"default":"$id.$key.params.yaml"
}
}
},

2
target/nextflow/workflows/runner/.config.vsh.yaml
View File

@@ -221,7 +221,7 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/utils/listInputDir"

2
target/nextflow/workflows/runner/main.nf
View File

@@ -3317,7 +3317,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
View File

@@ -214,7 +214,7 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"

2
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3319,7 +3319,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/well_metadata/.config.vsh.yaml
View File

@@ -212,7 +212,7 @@ build_info:
output: "target/nextflow/workflows/well_metadata"
executable: "target/nextflow/workflows/well_metadata/main.nf"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/workflows/well_metadata/main.nf
View File

@@ -3299,7 +3299,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_metadata",
"viash_version" : "0.9.2",
"git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
"git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {