Skip to content

Find ConvertSequencingArtifactToOxoG files properly. Fix for indexcov issue. #1310

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

Merged
merged 5 commits into from
Mar 5, 2021
Merged

Find ConvertSequencingArtifactToOxoG files properly. Fix for indexcov issue. #1310

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
c3c7bc0
Find ConvertSequencingArtifactToOxoG files.
roryk Oct 2, 2020
13c2f23
Fix goleft_indexcov issues.
roryk Oct 6, 2020
f2a0cac
Fix merge conflicts
ewels Mar 4, 2021
fd7a48b
Refactor #1310 - use regex group instead of code duplication
ewels Mar 4, 2021
ba3cdfc
Merge branch 'master' into master
ewels Mar 4, 2021
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
3 changes: 3 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,8 @@ For further information, please see the [documentation](https://multiqc.info/doc
- Add support for the creation of a "Reported vs Empirical Quality" graph to the Base Recalibration module.
- **hap.py**
- Updated module to plot both SNP and INDEL stats ([#1241](https://github.com/ewels/MultiQC/issues/1241))
- **indexcov**
- Fixed bug when making the PED file plots ([#1265](https://github.com/ewels/MultiQC/issues/1265))
- **Kaiju**
- Fixed bug affecting inputs with taxa levels other than Phylum ([#1217](https://github.com/ewels/MultiQC/issues/1217))
- Rework barplot, add top 5 taxons ([#1219](https://github.com/ewels/MultiQC/issues/1219))
Expand All @@ -75,6 +77,7 @@ For further information, please see the [documentation](https://multiqc.info/doc
- Display contig names in _Coverage per contig_ plot tooltip
- **Picard**
- Fix `HsMetrics` bait percentage columns ([#1212](https://github.com/ewels/MultiQC/issues/1212))
- Fix `ConvertSequencingArtifactToOxoG` files not being found ([#1310](https://github.com/ewels/MultiQC/issues/1310))
- Make `WgsMetrics` histogram smoothed if more than 1000 data points (avoids huge plots that crash the browser)
- Multiple new config options for `WgsMetrics` to customise coverage histogram and speed up MultiQC with very high coverage files.
- **PycoQC**
Expand Down
2 changes: 1 addition & 1 deletion multiqc/modules/picard/OxoGMetrics.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def parse_reports(self):
context_col = None

# Pull sample name from input
fn_search = re.search(r"INPUT(?:=|\s+)(\[?[^\s]+\]?)", l, flags=re.IGNORECASE)
fn_search = re.search(r"INPUT(?:_BASE)?(?:=|\s+)(\[?[^\s]+\]?)", l, flags=re.IGNORECASE)
if fn_search:
s_name = os.path.basename(fn_search.group(1).strip("[]"))
s_name = self.clean_s_name(s_name, f["root"])
Expand Down
2 changes: 1 addition & 1 deletion multiqc/plots/linegraph.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,7 @@ def plot(data, pconfig=None):
return get_template_mod().linegraph(plotdata, pconfig)
except (AttributeError, TypeError):
if config.plots_force_flat or (
not config.plots_force_interactive and len(plotdata[0]) > config.plots_flat_numseries
not config.plots_force_interactive and plotdata and len(plotdata[0]) > config.plots_flat_numseries
):
try:
return matplotlib_linegraph(plotdata, pconfig)
Expand Down