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Minor fixes to metadata #35

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merged 5 commits into from
Nov 2, 2023
Merged

Minor fixes to metadata #35

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222ee32
fix: use basename for stub files
kelly-sovacool Nov 2, 2023
481e075
chore: Merge branch 'main' into champagne-qc-fixes
kelly-sovacool Nov 2, 2023
f6ea4dc
fix: add biopython license
kelly-sovacool Nov 2, 2023
ed7e62b
docs: handle empty licen[cs]e field
kelly-sovacool Nov 2, 2023
a5d1701
docs: fix typo
kelly-sovacool Nov 2, 2023
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6 changes: 4 additions & 2 deletions docs/templates/modules.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ code_symbol <- '{{< fa regular file-code >}}'

if ('tools' %in% names(meta)) {
tools_df <- meta$tools %>% yaml_to_df()
for (colname in c('tool_dev_url', 'homepage', 'documentation')) {
for (colname in c('tool_dev_url', 'homepage', 'documentation', 'licence')) {
if (!(colname %in% colnames(tools_df))) {
tools_df[colname] <- NA_character_
}
Expand All @@ -69,7 +69,9 @@ if ('tools' %in% names(meta)) {
TRUE ~ ""),
code = case_when(!is.na(tool_dev_url) ~ glue("[{ code_symbol } Code]({ tool_dev_url })"),
TRUE ~ ""),
links = paste(home, docs, code, glue("`{ licence }`"),
license = case_when(!is.na(licence) ~ glue("`{ licence }`"),
TRUE ~ ""),
links = paste(home, docs, code, license,
sep = " &ensp; "),
markdown = glue("{ name }", "{ links }", "{ description }",
.sep = '\n\n')
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1 change: 1 addition & 0 deletions modules/CCBR/custom/countfastq/meta.yml
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Expand Up @@ -12,6 +12,7 @@ tools:
homepage: https://biopython.org/
tool_dev_url: https://github.com/biopython/biopython
doi: 10.1093/bioinformatics/btp163
licence: ["BSD 3-Clause"]
input:
- meta:
type: map
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2 changes: 1 addition & 1 deletion modules/CCBR/samtools/flagstat/main.nf
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Expand Up @@ -34,7 +34,7 @@ process SAMTOOLS_FLAGSTAT {
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix ?: "${bam.baseName}"
"""
touch ${prefix}.flagstat

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