Support input read-sets being paired-end

bin/check_fetchngs_samplesheet.py

@@ -35,6 +35,7 @@ def __init__(
         platform_col="instrument_platform",
         library_col="library_strategy",
         file1_col="fastq_1",
+        file2_col="fastq_2",
         **kwargs,
     ):
         """
@@ -49,13 +50,16 @@ def __init__(
                 of the instrument (default "instrument_platform").
             library_col (str): The name of the column that contains the strategy of the
                 preparation of the library (default "library_strategy").
+            file2_col (str): The name of the column that contains the second file path
+                for the paired-end read data (default "fastq_2").
         """
         super().__init__(**kwargs)
         self._accession_col = accession_col
         self._model_col = model_col
         self._platform_col = platform_col
         self._library_col = library_col
         self._file1_col = file1_col
+        self._file2_col = file2_col
         self._seen = set()
         self.modified = []
 
@@ -83,6 +87,8 @@ def _validate_file(self, row):
         if len(row[self._file1_col]) <= 0:
             raise AssertionError("Data file is required.")
         self._validate_data_format(row[self._file1_col])
+        if row[self._file2_col]:
+            self._validate_data_format(row[self._file2_col])
 
     def _validate_data_format(self, filename):
         """Assert that a given filename has one of the expected FASTQ extensions."""
@@ -165,7 +171,7 @@ def check_samplesheet(file_in, file_out):
         https://raw.githubusercontent.com/sanger-tol/blobtoolkit/main/assets/test/samplesheet.csv
 
     """
-    required_columns = {"run_accession", "instrument_model", "instrument_platform", "library_strategy", "fastq_1"}
+    required_columns = {"run_accession", "instrument_model", "instrument_platform", "library_strategy", "fastq_1", "fastq_2"}
     # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`.
     with file_in.open(newline="") as in_handle:
         reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))

modules.json

@@ -17,6 +17,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/busco/busco.diff"
                     },
+                    "cat/cat": {
+                        "branch": "master",
+                        "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2",
+                        "installed_by": ["modules"]
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",