vsh/demultiplex
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (d3a9c9b)

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

6
CHANGELOG.md
View File

@@ -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
## Major updates

6
src/dataflow/gather_fastqs_and_validate/main.nf
View File

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

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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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="2024-12-11T09:14:04Z"
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.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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="2024-12-11T09:14:04Z"
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.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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="2024-12-11T09:14:04Z"
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.revision="b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
LABEL org.opencontainers.image.revision="d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3"
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
},
"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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
package_config:
name: "demultiplex"
version: "main"

12
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" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3"
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
},
"package_config" : {
"name" : "demultiplex",
@@ -3042,9 +3042,9 @@ workflow run_wf {
println "Encountered next header '[${start_parsing}]', stopping parsing."
return true
}
// [Data] for illumina
// [Data], [BCLConvert_Data] for illumina
// [Samples] for Element Biosciences
if (header in ["Data", "Samples"]) {
if (header in ["Data", "Samples", "BCLConvert_Data"]) {
println "Found header [${header}], start parsing."
start_parsing = true
return
@@ -3069,7 +3069,7 @@ workflow run_wf {
return
}
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:
"Sample information file does not seem to contain any information about the samples!"
println "Finished processing run information file, found samples: ${samples}."

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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
dependencies:
- "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate"

6
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" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3"
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
},
"package_config" : {
"name" : "demultiplex",

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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3"
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
},
"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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3"
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
},
"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: "b7e30f394e7a4ae7a51961ade824e24ffe718e1f"
git_remote: "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-8-gb7e30f3"
git_commit: "d3a9c9b3be9790bf89258b14c9a8c83af945ad47"
git_remote: "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-9-gd3a9c9b"
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" : "b7e30f394e7a4ae7a51961ade824e24ffe718e1f",
"git_remote" : "https://x-access-token:ghs_PoDtMpilpQnn1Nk8WgE3ZAlxTrfk790lUeZy@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-8-gb7e30f3"
"git_commit" : "d3a9c9b3be9790bf89258b14c9a8c83af945ad47",
"git_remote" : "https://x-access-token:ghs_LDdnPEXvHVhqremDw1GFS68naiYOck2oDbCt@github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-9-gd3a9c9b"
},
"package_config" : {
"name" : "demultiplex",

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

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

6
target/nextflow/runner/main.nf
View File

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