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Build branch main with version main (5c096fc)

Browse Source 
Build pipeline: viash-hub.demultiplex.main-svj8q

Source commit: 5c096fce40

Source message: Fixes for v0.3.0 (#27)

Co-authored-by: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
This commit is contained in:
CI
2024-12-11 15:44:12 +00:00
parent 0e0262257b
commit 2121a3ac1c
25 changed files with 173 additions and 63 deletions
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6
CHANGELOG.md
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@@ -1,9 +1,15 @@
# demultiplex v0.3.1
# Minor updates
* Add `--run_information` and `--demultiplexer` arguments to `runner` workflow (PR #27).
# Bug fixes
* Fix detection of sample IDs from Illumina V2 sample sheets (PR #28).
* Provide a clear error message when `--run_information` is provided but not `--demultiplexer` (PR #27).
# demultiplex v0.3.0
## Major updates

9
src/demultiplex/main.nf
View File

@@ -25,6 +25,11 @@ workflow run_wf {
| map {id, state ->
def newState = [:]
println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
// No auto-detection of run information file (it is user provided),
// in this case the demultiplexer should also be specified.
assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
"you must also provide a demultiplexer"
if (!state.run_information) {
println("Run information was not specified, auto-detecting...")
// The supported_platforms hashmap must be a 1-on-1 mapping
@@ -62,7 +67,7 @@ workflow run_wf {
"found in input directory."
// When autodetecting, the demultiplexer must be set if the run information was found
assert demultiplexer, "State error: the demultiplexer should have been autodetected. " +
assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
"Please report this as a bug."
// When autodetecting, the found demultiplexer must match
@@ -82,7 +87,7 @@ workflow run_wf {
"run_information": run_information,
"demultiplexer": demultiplexer,
]
}
} // end auto-detection logic
if (newState.demultiplexer in ["bclconvert"]) {
// Do not add InterOp to state because we generate the summary csv's in the next

18
src/runner/config.vsh.yaml
View File

@@ -7,6 +7,24 @@ argument_groups:
description: Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/`
type: file
required: true
- name: --run_information
description: |
CSV file containing sample information, which will be used as
input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)
or 'RunManifest.csv' (Element Biosciences). If not specified,
will try to autodetect the sample sheet in the input directory.
Requires --demultiplexer to be set.
type: file
required: false
- name: "--demultiplexer"
type: string
required: false
choices: ["bases2fastq", "bclconvert"]
description: |
Demultiplexer to use, choice depends on the provider
of the instrument that was used to generate the data.
When not using --sample_sheet, specifying this argument is not
required.
- name: Annotation flags
arguments:
- name: --add_date_time

4
src/runner/main.nf
View File

@@ -12,9 +12,11 @@ workflow run_wf {
| demultiplex.run(
fromState: [
"input": "input",
"run_information": "run_information",
"demultiplexer": "demultiplexer",
"output": "fastq",
"output_falco": "qc/fastqc",
"output_multiqc": "qc/multiqc_report.html",
"output_multiqc": "qc/multiqc_report.html"
],
toState: { id, result, state ->
state + result

6
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -141,9 +141,9 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
View File

@@ -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/
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2024-12-11T14:07:52Z"
LABEL org.opencontainers.image.created="2024-12-11T15:28:43Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/io/publish/.config.vsh.yaml
View File

@@ -170,9 +170,9 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/publish/publish
View File

@@ -482,9 +482,9 @@ 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="2024-12-11T14:07:53Z"
LABEL org.opencontainers.image.created="2024-12-11T15:28:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/io/untar/.config.vsh.yaml
View File

@@ -148,9 +148,9 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/untar/untar
View File

@@ -476,9 +476,9 @@ 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="2024-12-11T14:07:53Z"
LABEL org.opencontainers.image.created="2024-12-11T15:28:44Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -139,9 +139,9 @@ build_info:
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

6
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -2972,9 +2972,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
View File

@@ -133,9 +133,9 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

6
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -2965,9 +2965,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/demultiplex/.config.vsh.yaml
View File

@@ -220,9 +220,9 @@ build_info:
output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
dependencies:
- "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate"

15
target/nextflow/demultiplex/main.nf
View File

@@ -3088,9 +3088,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",
@@ -3169,6 +3169,11 @@ workflow run_wf {
| map {id, state ->
def newState = [:]
println("Provided run information: ${state.run_information} and demultiplexer: ${state.demultiplexer}")
// No auto-detection of run information file (it is user provided),
// in this case the demultiplexer should also be specified.
assert (!state.run_information || state.demultiplexer): "When setting --run_information, " +
"you must also provide a demultiplexer"
if (!state.run_information) {
println("Run information was not specified, auto-detecting...")
// The supported_platforms hashmap must be a 1-on-1 mapping
@@ -3206,7 +3211,7 @@ workflow run_wf {
"found in input directory."
// When autodetecting, the demultiplexer must be set if the run information was found
assert demultiplexer, "State error: the demultiplexer should have been autodetected. " +
assert demultiplexer: "State error: the demultiplexer should have been autodetected. " +
"Please report this as a bug."
// When autodetecting, the found demultiplexer must match
@@ -3226,7 +3231,7 @@ workflow run_wf {
"run_information": run_information,
"demultiplexer": demultiplexer,
]
}
} // end auto-detection logic
if (newState.demultiplexer in ["bclconvert"]) {
// Do not add InterOp to state because we generate the summary csv's in the next

6
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -141,9 +141,9 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

6
target/nextflow/io/interop_summary_to_csv/main.nf
View File

@@ -2977,9 +2977,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/io/publish/.config.vsh.yaml
View File

@@ -170,9 +170,9 @@ build_info:
output: "target/nextflow/io/publish"
executable: "target/nextflow/io/publish/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

6
target/nextflow/io/publish/main.nf
View File

@@ -3012,9 +3012,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",

6
target/nextflow/io/untar/.config.vsh.yaml
View File

@@ -148,9 +148,9 @@ build_info:
output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
package_config:
name: "demultiplex"
version: "main"

6
target/nextflow/io/untar/main.nf
View File

@@ -2989,9 +2989,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/untar",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",

32
target/nextflow/runner/.config.vsh.yaml
View File

@@ -13,6 +13,32 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--run_information"
description: "CSV file containing sample information, which will be used as \n\
input for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\n\
or 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect\
\ the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--demultiplexer"
description: "Demultiplexer to use, choice depends on the provider\nof the instrument\
\ that was used to generate the data.\nWhen not using --sample_sheet, specifying\
\ this argument is not\nrequired.\n"
info: null
required: false
choices:
- "bases2fastq"
- "bclconvert"
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Annotation flags"
arguments:
- type: "boolean_true"
@@ -156,9 +182,9 @@ build_info:
output: "target/nextflow/runner"
executable: "target/nextflow/runner/main.nf"
viash_version: "0.9.0"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
git_commit: "5c096fce4015435019d81e2cc524a478f4034adc"
git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-10-g5c096fc"
dependencies:
- "target/nextflow/demultiplex"
- "target/nextflow/io/publish"

34
target/nextflow/runner/main.nf
View File

@@ -2820,6 +2820,30 @@ meta = [
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--run_information",
"description" : "CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called 'SampleSheet.csv' (Illumina)\nor 'RunManifest.csv' (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n",
"must_exist" : true,
"create_parent" : true,
"required" : false,
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "string",
"name" : "--demultiplexer",
"description" : "Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
"required" : false,
"choices" : [
"bases2fastq",
"bclconvert"
],
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
}
]
},
@@ -3003,9 +3027,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/runner",
"viash_version" : "0.9.0",
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
"git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc",
"git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-10-g5c096fc"
},
"package_config" : {
"name" : "demultiplex",
@@ -3065,9 +3089,11 @@ workflow run_wf {
| demultiplex.run(
fromState: [
"input": "input",
"run_information": "run_information",
"demultiplexer": "demultiplexer",
"output": "fastq",
"output_falco": "qc/fastqc",
"output_multiqc": "qc/multiqc_report.html",
"output_multiqc": "qc/multiqc_report.html"
],
toState: { id, result, state ->
state + result

22
target/nextflow/runner/nextflow_schema.json
View File

@@ -23,6 +23,28 @@
}
,
"run_information": {
"type":
"string",
"description": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer",
"help_text": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called \u0027SampleSheet.csv\u0027 (Illumina)\nor \u0027RunManifest.csv\u0027 (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
}
,
"demultiplexer": {
"type":
"string",
"description": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data",
"help_text": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
"enum": ["bases2fastq", "bclconvert"]
}
}
},