Merge pull request #21 from peterk87/fix-viralrecon-medaka

Fix for nf-core/viralrecon Medaka VCF sample extraction
peterk87 · Mar 18, 2022 · b9c3d1c · b9c3d1c
2 parents c65afa6 + 5376928
commit b9c3d1c
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Showing 6 changed files with 12 additions and 5 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.1
+current_version = 0.6.2
 commit = True
 tag = True
 

diff --git a/setup.py b/setup.py
@@ -60,6 +60,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/peterk87/xlavir',
-    version='0.6.1',
+    version='0.6.2',
     zip_safe=False,
 )
diff --git a/xlavir/__init__.py b/xlavir/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Peter Kruczkiewicz"""
 __email__ = '[email protected]'
-__version__ = '0.6.1'
+__version__ = '0.6.2'
diff --git a/xlavir/io/xl.py b/xlavir/io/xl.py
@@ -127,19 +127,24 @@ def write_xlsx_report(dfs: List[ExcelSheetDataFrame],
                                                                          include_header=esdf.include_header_width),
                                                           idx_and_cols)):
                     if col_name in float_cols:
+                        logger.debug(f'{esdf.sheet_name}|Column {col_name} ({i}) width = {width}')
                         sheet.set_column(i, i, width, monospace_float_fmt)
                     elif col_name in perc_cols:
+                        logger.debug(f'{esdf.sheet_name}|Column {col_name} ({i}) width = {width}')
                         sheet.set_column(i, i, width, monospace_perc_fmt)
                     elif col_name in perc_2dec_cols:
+                        logger.debug(f'{esdf.sheet_name}|Column {col_name} ({i}) width = {width}')
                         sheet.set_column(i, i, width, monospace_perc_2dec_fmt)
                     else:
+                        logger.debug(f'{esdf.sheet_name}|Column {col_name} ({i}) width = {width}')
                         sheet.set_column(i, i, width, monospace_fmt)
                 if not esdf.include_header_width:
                     for i, col_name in enumerate(idx_and_cols):
                         sheet.write_string(0, i, string=col_name, cell_format=header_with_wrap_fmt)
 
             elif esdf.column_widths:
                 for i, (width, col_name) in enumerate(zip(esdf.column_widths, idx_and_cols)):
+                    logger.debug(f'{esdf.sheet_name}|Column {col_name} ({i}) width = {width}')
                     sheet.set_column(i, i, width, monospace_wrap_fmt)
 
                 for i, idx in enumerate(esdf.df.index, 1):
@@ -237,7 +242,7 @@ def write_xlsx_report(dfs: List[ExcelSheetDataFrame],
                                             max_type='max')}
                                  )
 
-        if images_for_sheets and not images_added:
+        if images_for_sheets is not None and not images_added:
             add_images(images_for_sheets, book)
 
     df_qc = get_qc_df(dfs)

diff --git a/xlavir/tools/pangolin.py b/xlavir/tools/pangolin.py
@@ -9,10 +9,11 @@
 
 logger = logging.getLogger(__name__)
 
-PANGOLIN_CSV = 'pangolin.lineage_report.csv'
+PANGOLIN_CSV = 'pangolin.csv'
 
 PANGOLIN_GLOB_PATTERNS = [
     '**/*.pangolin.csv',
+    '**/pangolin.csv',
 ]
 
 PANGOLIN_SAMPLE_NAME_CLEANUP = [

diff --git a/xlavir/tools/variants.py b/xlavir/tools/variants.py
@@ -186,6 +186,7 @@ class VariantCaller(Enum):
     re.compile(r'\.longshot'),
     re.compile(r'\.snpeff'),
     re.compile(r'\.no_fs'),
+    re.compile(r'\.merged'),
 ]
 
 SNPSIFT_GLOB_PATTERNS = [