Skip to content

Improve mirtop stats script with GFF check #11262

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
d-jch wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Improve mirtop stats script with GFF check #11262

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
16 changes: 11 additions & 5 deletions modules/nf-core/mirtop/stats/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,11 +23,17 @@ process MIRTOP_STATS {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mirtop \\
stats \\
$args \\
--out stats \\
$mirtop_gff
mkdir -p stats
if grep -qv "^#" "$mirtop_gff"; then
mirtop \\
stats \\
$args \\
--out stats \\
$mirtop_gff
else
touch stats/mirtop_stats.txt
touch stats/mirtop_stats.log
fi
Comment on lines +27 to +36
Copy link
Copy Markdown
Contributor

@famosab famosab Apr 27, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The input file should be present if someone wants to run this module so I do not get your proposed change?


mv stats/mirtop_stats.log stats/${prefix}_stats.log
mv stats/mirtop_stats.txt stats/${prefix}_stats.txt
Expand Down