Skip to content

Updating tools/bioconductor-scp from version 1.16.0 to 1.20.0 #777

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gxydevbot wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Updating tools/bioconductor-scp from version 1.16.0 to 1.20.0 #777

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
486e5c7
Updating tools/bioconductor-scp from version 1.16.0 to 1.20.0
Jun 22, 2026
6f2b45b
Merge branch 'master' into tools/bioconductor-scp
hechth Jul 10, 2026
f6b628e
Merge branch 'master' into tools/bioconductor-scp
hechth Jul 22, 2026
1cb4b6e
updated dependencies
hechth Jul 22, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 6 additions & 7 deletions tools/bioconductor-scp/bioconductor_scp.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,15 @@
</xrefs>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">bioconductor-scp</requirement>
<requirement type="package" version="1.84.0">bioconductor-impute</requirement>
<requirement type="package" version="3.54.0">bioconductor-sva</requirement>
<requirement type="package" version="1.80.0">bioconductor-impute</requirement>
<requirement type="package" version="1.34.0">bioconductor-scater</requirement>
<requirement type="package" version="1.16.0">bioconductor-qfeatures</requirement>
<requirement type="package" version="3.62.1">bioconductor-limma</requirement>
<requirement type="package" version="3.5.1">r-ggplot2</requirement>
<requirement type="package" version="1.38.0">bioconductor-scater</requirement>
</requirements>
<required_files>
<include path="utils.r" />
</required_files>
<expand macro="creator" />
<command detect_errors="exit_code"><![CDATA[
<command detect_errors="aggressive"><![CDATA[
echo ${run_script} &&
Rscript -e 'source("${__tool_directory__}/utils.r")' -e 'source("${run_script}")'
#if $data_export.export_R_script
Expand All @@ -29,6 +26,8 @@
]]></command>
<configfiles>
<configfile name="run_script"><![CDATA[
options(error = function() traceback(3))

data_input <- read.delim("$input_data", sep="\t")
metadata <- read.delim("$input_annotations", sep="\t")
runCol <- colnames(data_input)[$runcol]
Expand Down Expand Up @@ -145,7 +144,7 @@
SummarizedExperiment::colData(scp)[["MedianRI"]] <- medians

#if $generate_QC_plots
QC_medianRI <- SummarizedExperimentcolData(scp) |>
QC_medianRI <- SummarizedExperiment::colData(scp) |>
data.frame() |>
ggplot2::ggplot() +
ggplot2::aes(x = MedianRI,
Expand Down
2 changes: 1 addition & 1 deletion tools/bioconductor-scp/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">1.16.0</token>
<token name="@TOOL_VERSION@">1.20.0</token>
<xml name="creator">
<creator>
<person
Expand Down
Loading