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Support modules with exec: blocks #3633

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Merged
mirpedrol merged 4 commits into from
Aug 1, 2025
Merged

Support modules with exec: blocks #3633

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05c52e6
Support modules with exec: blocks
muffato Jun 20, 2025
6975c28
[automated] Update CHANGELOG.md
nf-core-bot Jun 20, 2025
840d0d9
Merge branch 'dev' into module_exec
muffato Jul 16, 2025
2872af9
Merge branch 'dev' into module_exec
mirpedrol Aug 1, 2025
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Support modules with exec: blocks
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@muffato
muffato committed Jun 20, 2025
commit 05c52e6c158eecddc053f3f0e487128850509b55
12 changes: 10 additions & 2 deletions nf_core/modules/lint/main_nf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,7 @@ def main_nf(
process_lines = []
script_lines = []
shell_lines = []
exec_lines = []
when_lines = []
iter_lines = iter(lines)
for line in iter_lines:
Expand All @@ -110,6 +111,9 @@ def main_nf(
if re.search(r"^\s*shell\s*:", line) and state in ["input", "output", "when", "process"]:
state = "shell"
continue
if re.search(r"^\s*exec\s*:", line) and state in ["input", "output", "when", "process"]:
state = "exec"
continue

# Perform state-specific linting checks
if state == "process" and not _is_empty(line):
Expand All @@ -132,6 +136,8 @@ def main_nf(
script_lines.append(line)
if state == "shell" and not _is_empty(line):
shell_lines.append(line)
if state == "exec" and not _is_empty(line):
exec_lines.append(line)

# Check that we have required sections
if not len(outputs):
Expand All @@ -149,8 +155,10 @@ def main_nf(
check_when_section(module, when_lines)

# Check that we have script or shell, not both
if len(script_lines) and len(shell_lines):
module.failed.append(("main_nf_script_shell", "Script and Shell found, should use only one", module.main_nf))
if sum(bool(block_lines) for block_lines in (script_lines, shell_lines, exec_lines)) > 1:
module.failed.append(
("main_nf_script_shell", "Multiple script:/shell:/exec: blocks found, should use only one", module.main_nf)
)

# Check the script definition
if len(script_lines):
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