Build branch main with version main (a948c26)

Build pipeline: viash-hub.htrnaseq.main-qpqxt

Source commit: a948c26193

Source message: Bump viash to 0.9.4 (#51)
This commit is contained in:
CI
2025-04-29 13:35:02 +00:00
parent a95268a2b5
commit ccd3e04ddc
65 changed files with 1087 additions and 865 deletions

View File

@@ -202,8 +202,8 @@ build_info:
engine: "docker|native"
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -213,7 +213,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# create_eset main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
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="2025-04-29T11:22:40Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -179,8 +179,8 @@ build_info:
engine: "docker|native"
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -190,7 +190,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# create_fdata main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -458,9 +458,9 @@ 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="2025-04-29T11:22:40Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -193,8 +193,8 @@ build_info:
engine: "docker|native"
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -204,7 +204,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# create_pdata main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -458,9 +458,9 @@ 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="2025-04-29T11:22:41Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -151,8 +151,8 @@ build_info:
engine: "docker|native"
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -162,7 +162,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# check_eset main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
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="2025-04-29T11:22:39Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -160,8 +160,8 @@ build_info:
engine: "docker|native"
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: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -171,7 +171,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# check_cutadapt_output main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -457,9 +457,9 @@ 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="2025-04-29T11:22:41Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -135,8 +135,8 @@ build_info:
engine: "docker|native"
output: "target/executable/io/publish_fastqs"
executable: "target/executable/io/publish_fastqs/publish_fastqs"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -146,7 +146,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# publish_fastqs main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -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_fastqs"
LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -189,8 +189,8 @@ build_info:
engine: "docker|native"
output: "target/executable/io/publish_results"
executable: "target/executable/io/publish_results/publish_results"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -200,7 +200,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# publish_results main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -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_results"
LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -281,8 +281,8 @@ build_info:
engine: "docker|native"
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -292,7 +292,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# parallel_map main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -461,9 +461,9 @@ 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="2025-04-29T11:22:41Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -211,8 +211,8 @@ build_info:
engine: "docker|native"
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -222,7 +222,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# create_report main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
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="2025-04-29T11:22:41Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -283,15 +283,31 @@ plateLayout <- function(
if (is.null(colours)) {
colours <- tryCatch({
colorRamp2(
circlize::colorRamp2(
breaks = breaks,
colors = brewer.pal(length(breaks), "Purples")
)
},
error = function(cond) {
return(c("#9370DB", "white"))
error = function(cond){
message("Recomputed breaks for proper colour mapping")
breakValues <- plateValues$values
breakValues[which(is.na(breakValues))] <- 0
if (all(breakValues >= 0)) {
breaks <- computeBreaks(7, max(plateValues$values, na.rm = TRUE))
} else {
breaks <- quantile(plateValues$values, probs = seq(0, 1, 0.125))
}
circlize::colorRamp2(
breaks = breaks,
colors = brewer.pal(length(breaks), "Purples")
)
})
}
ht <- Heatmap(
plateValues$values,
column_title = mainTitle, column_title_side = "top",
@@ -425,6 +441,7 @@ computeBreaks <- function(nBreaks, variable) {
)
coefExp <- c(exp(coefSystem[1]), coefSystem[2])
breaks <- coefExp[1] * exp((1:(nBreaks - 1)) * coefExp[2])
breaks <- unique(c(0, breaks))
}
return(c(0, breaks))
}
return(breaks)
}

View File

@@ -200,8 +200,8 @@ build_info:
engine: "docker|native"
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -211,7 +211,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# combine_star_logs main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -457,9 +457,9 @@ 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="2025-04-29T11:22:39Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:55Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -184,8 +184,8 @@ build_info:
engine: "docker|native"
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -195,7 +195,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# generate_pool_statistics main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -458,9 +458,9 @@ 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="2025-04-29T11:22:40Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

View File

@@ -266,8 +266,8 @@ build_info:
engine: "docker|native"
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.2"
git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
viash_version: "0.9.4"
git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -277,7 +277,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.2"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:

View File

@@ -2,7 +2,7 @@
# generate_well_statistics main
#
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -461,9 +461,9 @@ 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="2025-04-29T11:22:39Z"
LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER