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Remove nf-core modules check #878

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Mar 15, 2021
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f38b5d0
Remove nf-core modules check
ewels Mar 15, 2021
910e139
Comment out 'nf-core modules update' cli command for now
ewels Mar 15, 2021
7d527e6
Modules install + remove - exit if an invalid directory
ewels Mar 15, 2021
bcd6f62
Create - rename .github/filters.yml to tests/pytest_include.yml
ewels Mar 15, 2021
2c64007
Add awesome fuzzy-finder for nf-core modules install
ewels Mar 15, 2021
91a82a3
modules list - output rich table or JSON
ewels Mar 15, 2021
210282d
nf-core modules list - print local installed modules
ewels Mar 15, 2021
9c7a491
Fix pytest_include.yml path
ewels Mar 15, 2021
df24e78
Blacken
ewels Mar 15, 2021
0d96227
Fix pytests
ewels Mar 15, 2021
37e34ab
Fix merge conflicts, use pytest_software.yml
ewels Mar 15, 2021
f493287
Cut down cli help text length for nf-core modules create
ewels Mar 15, 2021
336de7d
Drop 'process' directory when creating a new local module
ewels Mar 15, 2021
ab5c1e2
Remove linebreaks from module template around prefix
ewels Mar 15, 2021
cf4a78f
Update main.nf
drpatelh Mar 15, 2021
e212eba
Create - fix bug when conda package not found for meta info.
ewels Mar 15, 2021
55fe76d
Modules template - remove example command flags
ewels Mar 15, 2021
4fb0895
Module create - strip cookiecutter template structure back
ewels Mar 15, 2021
fef60f5
modules create - switch to jinja2 instead of cookiecutter
ewels Mar 15, 2021
7b09297
Use |upper filter instead of variable specially for uppercase
ewels Mar 15, 2021
94c614b
Just throw all object attributes at the jinja template
ewels Mar 15, 2021
50b3be5
Linebreaks in test main.nf
ewels Mar 15, 2021
464260a
Added more help text explaining links
ewels Mar 15, 2021
fc1e45f
Update example test data path
ewels Mar 15, 2021
17db9a5
Log about PROFILE, fix tests bug with import path for no subtool
ewels Mar 15, 2021
b08dbb0
Test yml builder - fix minor yaml output issues
ewels Mar 15, 2021
19da126
Update pytest with new path
ewels Mar 15, 2021
494477f
Add back example flags if using meta
ewels Mar 15, 2021
5e82962
modules create-test-yml - prompt to set profile to docker, singularit…
ewels Mar 15, 2021
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Use |upper filter instead of variable specially for uppercase
  • Loading branch information
ewels committed Mar 15, 2021
commit 7b09297e02be9fc5a68be02986d1ac861470916d
2 changes: 1 addition & 1 deletion nf_core/module-template/software/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)

process {{ tool_name_upper }} {
process {{ tool_name|upper }} {
{{ 'tag "$meta.id"' if has_meta else "'$bam'" }}
label '{{ label }}'
publishDir "${params.outdir}",
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4 changes: 2 additions & 2 deletions nf_core/module-template/tests/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

nextflow.enable.dsl = 2

include { {{ tool_name_upper }} } from '../../../../software/{{ tool_dir }}/main.nf' addParams( options: [:] )
include { {{ tool_name|upper }} } from '../../../../software/{{ tool_dir }}/main.nf' addParams( options: [:] )

workflow test_{{ tool_name }} {
{% if has_meta %}
Expand All @@ -13,5 +13,5 @@ workflow test_{{ tool_name }} {
def input = file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true)
{% endif %}

{{ tool_name_upper }} ( input )
{{ tool_name|upper }} ( input )
}
1 change: 0 additions & 1 deletion nf_core/modules/create.py
Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,6 @@ def render_template(self):
tool=self.tool,
subtool=self.subtool if self.subtool else "",
tool_name=self.tool_name,
tool_name_upper=self.tool_name.upper(),
tool_dir=self.tool_dir,
author=self.author,
bioconda=self.bioconda,
Expand Down