Build branch main with version main (d3a9c9b)

Build pipeline: viash-hub.demultiplex.main-gcqps

Source commit: d3a9c9b3be

Source message: Fix detection of sample names from Illumina V2 sample sheets (#28)
This commit is contained in:
CI
2024-12-11 14:22:44 +00:00
parent ef54635d93
commit 0e0262257b
22 changed files with 69 additions and 63 deletions

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@@ -1,3 +1,9 @@
# demultiplex v0.3.1
# Bug fixes
* Fix detection of sample IDs from Illumina V2 sample sheets (PR #28).
# demultiplex v0.3.0 # demultiplex v0.3.0
## Major updates ## Major updates

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@@ -29,9 +29,9 @@ workflow run_wf {
println "Encountered next header '[${start_parsing}]', stopping parsing." println "Encountered next header '[${start_parsing}]', stopping parsing."
return true return true
} }
// [Data] for illumina // [Data], [BCLConvert_Data] for illumina
// [Samples] for Element Biosciences // [Samples] for Element Biosciences
if (header in ["Data", "Samples"]) { if (header in ["Data", "Samples", "BCLConvert_Data"]) {
println "Found header [${header}], start parsing." println "Found header [${header}], start parsing."
start_parsing = true start_parsing = true
return return
@@ -56,7 +56,7 @@ workflow run_wf {
return return
} }
assert start_parsing: assert start_parsing:
"Sample information file does not contain [Data] or [Samples] header!" "Sample information file does not contain [Data], [Samples] or [BCLConvert_Data] header!"
assert samples.size() > 1: assert samples.size() > 1:
"Sample information file does not seem to contain any information about the samples!" "Sample information file does not seem to contain any information about the samples!"
println "Finished processing run information file, found samples: ${samples}." println "Finished processing run information file, found samples: ${samples}."

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@@ -141,9 +141,9 @@ build_info:
output: "target/executable/io/interop_summary_to_csv" output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -470,9 +470,9 @@ 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/ 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.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2024-12-11T09:14:04Z" LABEL org.opencontainers.image.created="2024-12-11T14:07:52Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f" LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
LABEL org.opencontainers.image.version="main" LABEL org.opencontainers.image.version="main"
VIASHDOCKER VIASHDOCKER

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@@ -170,9 +170,9 @@ build_info:
output: "target/executable/io/publish" output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish" executable: "target/executable/io/publish/publish"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -482,9 +482,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish" LABEL org.opencontainers.image.description="Companion container for running component io publish"
LABEL org.opencontainers.image.created="2024-12-11T09:14:04Z" LABEL org.opencontainers.image.created="2024-12-11T14:07:53Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f" LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
LABEL org.opencontainers.image.version="main" LABEL org.opencontainers.image.version="main"
VIASHDOCKER VIASHDOCKER

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@@ -148,9 +148,9 @@ build_info:
output: "target/executable/io/untar" output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar" executable: "target/executable/io/untar/untar"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -476,9 +476,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io untar" LABEL org.opencontainers.image.description="Companion container for running component io untar"
LABEL org.opencontainers.image.created="2024-12-11T09:14:04Z" LABEL org.opencontainers.image.created="2024-12-11T14:07:53Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f" LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
LABEL org.opencontainers.image.version="main" LABEL org.opencontainers.image.version="main"
VIASHDOCKER VIASHDOCKER

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@@ -139,9 +139,9 @@ build_info:
output: "target/nextflow/dataflow/combine_samples" output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf" executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -2972,9 +2972,9 @@ meta = [
"engine" : "native|native", "engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples", "output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",

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@@ -133,9 +133,9 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate" output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -2965,9 +2965,9 @@ meta = [
"engine" : "native|native", "engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",
@@ -3042,9 +3042,9 @@ workflow run_wf {
println "Encountered next header '[${start_parsing}]', stopping parsing." println "Encountered next header '[${start_parsing}]', stopping parsing."
return true return true
} }
// [Data] for illumina // [Data], [BCLConvert_Data] for illumina
// [Samples] for Element Biosciences // [Samples] for Element Biosciences
if (header in ["Data", "Samples"]) { if (header in ["Data", "Samples", "BCLConvert_Data"]) {
println "Found header [${header}], start parsing." println "Found header [${header}], start parsing."
start_parsing = true start_parsing = true
return return
@@ -3069,7 +3069,7 @@ workflow run_wf {
return return
} }
assert start_parsing: assert start_parsing:
"Sample information file does not contain [Data] or [Samples] header!" "Sample information file does not contain [Data], [Samples] or [BCLConvert_Data] header!"
assert samples.size() > 1: assert samples.size() > 1:
"Sample information file does not seem to contain any information about the samples!" "Sample information file does not seem to contain any information about the samples!"
println "Finished processing run information file, found samples: ${samples}." println "Finished processing run information file, found samples: ${samples}."

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@@ -220,9 +220,9 @@ build_info:
output: "target/nextflow/demultiplex" output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf" executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
dependencies: dependencies:
- "target/nextflow/io/untar" - "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate" - "target/nextflow/dataflow/gather_fastqs_and_validate"

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@@ -3088,9 +3088,9 @@ meta = [
"engine" : "native|native", "engine" : "native|native",
"output" : "target/nextflow/demultiplex", "output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",

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@@ -141,9 +141,9 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv" output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf" executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -2977,9 +2977,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv", "output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",

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@@ -170,9 +170,9 @@ build_info:
output: "target/nextflow/io/publish" output: "target/nextflow/io/publish"
executable: "target/nextflow/io/publish/main.nf" executable: "target/nextflow/io/publish/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -3012,9 +3012,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/io/publish", "output" : "target/nextflow/io/publish",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",

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@@ -148,9 +148,9 @@ build_info:
output: "target/nextflow/io/untar" output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf" executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
package_config: package_config:
name: "demultiplex" name: "demultiplex"
version: "main" version: "main"

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@@ -2989,9 +2989,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/io/untar", "output" : "target/nextflow/io/untar",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",

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@@ -156,9 +156,9 @@ build_info:
output: "target/nextflow/runner" output: "target/nextflow/runner"
executable: "target/nextflow/runner/main.nf" executable: "target/nextflow/runner/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f" git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex" git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3" git_tag: "v0.1.1-9-gd3a9c9b"
dependencies: dependencies:
- "target/nextflow/demultiplex" - "target/nextflow/demultiplex"
- "target/nextflow/io/publish" - "target/nextflow/io/publish"

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@@ -3003,9 +3003,9 @@ meta = [
"engine" : "native|native", "engine" : "native|native",
"output" : "target/nextflow/runner", "output" : "target/nextflow/runner",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f", "git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex", "git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3" "git_tag" : "v0.1.1-9-gd3a9c9b"
}, },
"package_config" : { "package_config" : {
"name" : "demultiplex", "name" : "demultiplex",