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mmassaviol
WAWmassaviol
Commits
3a82de07
Commit
3a82de07
authored
Sep 07, 2020
by
root
Browse files
Python: Fix generate snakefile
parent
8d7302a4
Changes
2
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Inline
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generate_workflow_snakefile.py
View file @
3a82de07
...
...
@@ -98,8 +98,12 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output
for
command
in
tool_yaml
[
"commands"
]:
if
command
[
"name"
]
==
step
[
"rule_name"
]:
for
output
in
command
[
"outputs"
]:
if
"{sample}"
in
output
[
"file"
]:
need_expand
=
True
if
"file"
in
output
:
if
"{sample}"
in
output
[
"file"
]:
need_expand
=
True
else
:
# TODO return error
continue
if
need_expand
:
expand_start
=
"expand("
expand_end
=
", sample=SAMPLES)"
...
...
tools/vcfparser/vcfparser.yaml
View file @
3a82de07
...
...
@@ -18,7 +18,7 @@
output_dir
:
vcfparser
,
inputs
:
[{
name
:
vcfs
,
type
:
"
vcf"
}],
outputs
:
[
{
name
:
vcf_plots_mqc
,
type
:
"
tsv"
}
{
name
:
vcf_plots_mqc
,
type
:
"
tsv"
,
file
:
"
vcf_plots_mqc_list.tsv"
}
#{ name: "List of plots files", file: "vcf_plots_mqc_list.tsv", description: "List of plots files generated and included in the final report" }
],
options
:
...
...
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