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Build branch runner_multiple_input_directories with version runner_multiple_input_directories (fc48924)

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Build pipeline: viash-hub.htrnaseq.runner-multiple-input-directories-xrw45

Source commit: fc48924aa8

Source message: Fix FASTQ paths
This commit is contained in:
CI
2025-02-11 20:11:42 +00:00
parent b201cc9045
commit 579a737d8c
60 changed files with 80 additions and 76 deletions
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2
src/workflows/runner/main.nf
View File

@@ -14,7 +14,7 @@ workflow run_wf {
| flatMap {id, state ->
// Create an input event per input directory
def new_state = state.input.withIndex().collect{input_dir, id_index ->
def state_item = state + ["input": input_dir, "index": id_index]
def state_item = state + ["input": input_dir, "index": id_index, "run_id": id]
return ["${id}_${id_index}".toString(), state_item]
}
return new_state

6
src/workflows/well_demultiplex/main.nf
View File

@@ -187,7 +187,8 @@ workflow run_wf {
[
input: state.output_r1,
gzip_output: false,
output: "${state.pool}/${state.barcode_id}_R1.fastq"
// Remark: the fastq path part may seem superfluous but is necessary for publising later
output: "fastq/${state.pool}/${state.barcode_id}_R1.fastq"
]
},
toState: { id, result, state ->
@@ -203,7 +204,8 @@ workflow run_wf {
[
input: state.output_r2,
gzip_output: false,
output: "${state.pool}/${state.barcode_id}_R2.fastq",
// Remark: the fastq path part may seem superfluous but is necessary for publising later
output: "fastq/${state.pool}/${state.barcode_id}_R2.fastq",
]
},
toState: { id, result, state ->

2
target/executable/eset/create_eset/.config.vsh.yaml
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@@ -198,7 +198,7 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -477,9 +477,9 @@ 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 eset create_eset"
LABEL org.opencontainers.image.created="2025-02-11T15:24:07Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -177,7 +177,7 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-02-11T15:24:08Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -191,7 +191,7 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-02-11T15:24:07Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -148,7 +148,7 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
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

@@ -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="2025-02-11T15:24:07Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -158,7 +158,7 @@ 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: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
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

@@ -476,9 +476,9 @@ 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="2025-02-11T15:24:07Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:22Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -143,7 +143,7 @@ build_info:
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -470,9 +470,9 @@ 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="2025-02-11T15:24:05Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:20Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -187,7 +187,7 @@ build_info:
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -484,9 +484,9 @@ 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="2025-02-11T15:24:06Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -279,7 +279,7 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/parallel_map/parallel_map
View File

@@ -540,9 +540,9 @@ 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="2025-02-11T15:24:08Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -201,7 +201,7 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-02-11T15:24:08Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -198,7 +198,7 @@ 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-02-11T15:24:05Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:20Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -182,7 +182,7 @@ 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-02-11T15:24:06Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -262,7 +262,7 @@ 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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="2025-02-11T15:24:07Z"
LABEL org.opencontainers.image.created="2025-02-11T19:25:21Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="b8bad5851d5d9c579d95ec2c382626a350d00d9e"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"
VIASHDOCKER

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

@@ -198,7 +198,7 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3072,7 +3072,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -177,7 +177,7 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3044,7 +3044,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -191,7 +191,7 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3058,7 +3058,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -148,7 +148,7 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
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

@@ -2997,7 +2997,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"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

@@ -158,7 +158,7 @@ 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: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
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

@@ -3009,7 +3009,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -143,7 +143,7 @@ build_info:
output: "target/nextflow/io/publish_fastqs"
executable: "target/nextflow/io/publish_fastqs/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -2983,7 +2983,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_fastqs",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -187,7 +187,7 @@ build_info:
output: "target/nextflow/io/publish_results"
executable: "target/nextflow/io/publish_results/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3032,7 +3032,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish_results",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -279,7 +279,7 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3144,7 +3144,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/report/create_report/.config.vsh.yaml
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@@ -201,7 +201,7 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3077,7 +3077,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -198,7 +198,7 @@ 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3060,7 +3060,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -182,7 +182,7 @@ 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3044,7 +3044,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -262,7 +262,7 @@ 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: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3135,7 +3135,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -147,7 +147,7 @@ build_info:
output: "target/nextflow/utils/listInputDir"
executable: "target/nextflow/utils/listInputDir/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -2983,7 +2983,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/utils/listInputDir",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

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

@@ -319,7 +319,7 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/stats/combine_star_logs"

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

@@ -3223,7 +3223,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/runner/.config.vsh.yaml
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@@ -197,7 +197,7 @@ build_info:
output: "target/nextflow/workflows/runner"
executable: "target/nextflow/workflows/runner/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/utils/listInputDir"

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

@@ -3057,7 +3057,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/runner",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3124,7 +3124,7 @@ workflow run_wf {
| flatMap {id, state ->
// Create an input event per input directory
def new_state = state.input.withIndex().collect{input_dir, id_index ->
def state_item = state + ["input": input_dir, "index": id_index]
def state_item = state + ["input": input_dir, "index": id_index, "run_id": id]
return ["${id}_${id_index}".toString(), state_item]
}
return new_state

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

@@ -211,7 +211,7 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"

8
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3084,7 +3084,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {
@@ -3322,7 +3322,8 @@ workflow run_wf {
[
input: state.output_r1,
gzip_output: false,
output: "${state.pool}/${state.barcode_id}_R1.fastq"
// Remark: the fastq path part may seem superfluous but is necessary for publising later
output: "fastq/${state.pool}/${state.barcode_id}_R1.fastq"
]
},
toState: { id, result, state ->
@@ -3338,7 +3339,8 @@ workflow run_wf {
[
input: state.output_r2,
gzip_output: false,
output: "${state.pool}/${state.barcode_id}_R2.fastq",
// Remark: the fastq path part may seem superfluous but is necessary for publising later
output: "fastq/${state.pool}/${state.barcode_id}_R2.fastq",
]
},
toState: { id, result, state ->

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

@@ -209,7 +209,7 @@ build_info:
output: "target/nextflow/workflows/well_metadata"
executable: "target/nextflow/workflows/well_metadata/main.nf"
viash_version: "0.9.0"
git_commit: "b8bad5851d5d9c579d95ec2c382626a350d00d9e"
git_commit: "fc48924aa82d885ede794fd8e19a3514206bbd2d"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

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

@@ -3064,7 +3064,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_metadata",
"viash_version" : "0.9.0",
"git_commit" : "b8bad5851d5d9c579d95ec2c382626a350d00d9e",
"git_commit" : "fc48924aa82d885ede794fd8e19a3514206bbd2d",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {