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Build branch update-readme with version update-readme (b963aed)

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Build pipeline: viash-hub.demultiplex.update-readme-54wrh

Source commit: b963aed523

Source message: update bucket
This commit is contained in:
CI
2025-05-06 09:25:57 +00:00
parent 26193da299
commit be1e2a54fc
21 changed files with 47 additions and 46 deletions
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13
README.qmd
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@@ -53,7 +53,7 @@ Two variants of the same workflow are provided, depending on the flexibility in
### Test data
We have provided test data at `gs://viash-hub-test-data/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2` (Illumina), but please feel free to bring your own. The URL of the test data can be provided as-is to the workflow, or you can download everything and specify a local path.
We have provided test data at `gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2` (Illumina), but please feel free to bring your own. The URL of the test data can be provided as-is to the workflow, or you can download everything and specify a local path.
The input data should follow the structure of either Illumina or Element Biosciences sequencers. The workflow will automatically detect which demultiplexer to use (`bclconvert` or `bases2fastq`) based on the
presence of either `SampleSheet.csv` or `RunParameters.xml` in the input directory. Demultiplexer can also be set explicitly using the `--demultiplexer` parameter.
@@ -79,7 +79,7 @@ Press the ‘Launch’ button and follow the instructions.
3. In the next step, we provide the paramters as follows and leave the rest as defalut:
- `input`:
`gs://viash-hub-test-data/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2`
`gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2`
![](assets/demultiplex-launch-parameters-2.png)
@@ -138,8 +138,8 @@ easiest is to use the integrated help functionality, for instance
using the following:
``` bash
nextflow run https://packages.viash-hub.com/vsh/demultiplex.git \
-revision v0.3.4 \
nextflow run vsh/demultiplex \
-revision v0.3.9 \
-main-script target/nextflow/workflows/runner/main.nf \
--help
```
@@ -150,11 +150,12 @@ Having this project available locally, you can run the following command:
nextflow run vsh/demultiplex \
-r v0.3.9 \
-main-script target/nextflow/runner/main.nf \
--input "gs://viash-hub-test-data/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2" \
--input "gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2" \
--demultiplexer bclconvert \
--skip_copycomplete_check \
--publish_dir example_output/ \
-profile docker \
-c labels.config
-c src/config/labels.config
```
### (Optional) Resource usage tuning

4
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
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@@ -151,9 +151,9 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
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@@ -454,9 +454,9 @@ 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/
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2025-05-06T07:42:19Z"
LABEL org.opencontainers.image.created="2025-05-06T09:10:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="d755985664a702ccc854d0cb3caa1f86166b669b"
LABEL org.opencontainers.image.revision="b963aed523a223ab3571d3c449901766c632811d"
LABEL org.opencontainers.image.version="update-readme"
VIASHDOCKER

4
target/executable/io/publish/.config.vsh.yaml
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@@ -199,9 +199,9 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/executable/io/publish/publish
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@@ -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"
LABEL org.opencontainers.image.created="2025-05-06T07:42:19Z"
LABEL org.opencontainers.image.created="2025-05-06T09:10:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="d755985664a702ccc854d0cb3caa1f86166b669b"
LABEL org.opencontainers.image.revision="b963aed523a223ab3571d3c449901766c632811d"
LABEL org.opencontainers.image.version="update-readme"
VIASHDOCKER

4
target/executable/io/untar/.config.vsh.yaml
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@@ -156,9 +156,9 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/executable/io/untar/untar
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@@ -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 untar"
LABEL org.opencontainers.image.created="2025-05-06T07:42:19Z"
LABEL org.opencontainers.image.created="2025-05-06T09:10:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="d755985664a702ccc854d0cb3caa1f86166b669b"
LABEL org.opencontainers.image.revision="b963aed523a223ab3571d3c449901766c632811d"
LABEL org.opencontainers.image.version="update-readme"
VIASHDOCKER

4
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
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@@ -165,9 +165,9 @@ build_info:
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/nextflow/dataflow/combine_samples/main.nf
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@@ -3230,9 +3230,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
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@@ -141,9 +141,9 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
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@@ -3203,9 +3203,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/demultiplex/.config.vsh.yaml
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@@ -247,9 +247,9 @@ build_info:
output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
dependencies:
- "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate"

4
target/nextflow/demultiplex/main.nf
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@@ -3350,9 +3350,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
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@@ -151,9 +151,9 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/nextflow/io/interop_summary_to_csv/main.nf
View File

@@ -3217,9 +3217,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/io/publish/.config.vsh.yaml
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@@ -199,9 +199,9 @@ build_info:
output: "target/nextflow/io/publish"
executable: "target/nextflow/io/publish/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/nextflow/io/publish/main.nf
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@@ -3274,9 +3274,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/io/untar/.config.vsh.yaml
View File

@@ -156,9 +156,9 @@ build_info:
output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
package_config:
name: "demultiplex"
version: "update-readme"

4
target/nextflow/io/untar/main.nf
View File

@@ -3227,9 +3227,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/untar",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/runner/.config.vsh.yaml
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@@ -195,9 +195,9 @@ build_info:
output: "target/nextflow/runner"
executable: "target/nextflow/runner/main.nf"
viash_version: "0.9.4"
git_commit: "d755985664a702ccc854d0cb3caa1f86166b669b"
git_commit: "b963aed523a223ab3571d3c449901766c632811d"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-28-gd755985"
git_tag: "v0.1.1-29-gb963aed"
dependencies:
- "target/nextflow/demultiplex"
- "target/nextflow/io/publish"

4
target/nextflow/runner/main.nf
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@@ -3270,9 +3270,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/runner",
"viash_version" : "0.9.4",
"git_commit" : "d755985664a702ccc854d0cb3caa1f86166b669b",
"git_commit" : "b963aed523a223ab3571d3c449901766c632811d",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-28-gd755985"
"git_tag" : "v0.1.1-29-gb963aed"
},
"package_config" : {
"name" : "demultiplex",