feat: Add entry suggestion to samplesheet check (#89)

beiko-lab · Apr 21, 2023 · 47e4f85 · 47e4f85
1 parent 4775118
commit 47e4f85
Showing 1 changed file with 26 additions and 8 deletions.
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -54,14 +54,23 @@ def check_samplesheet(file_in, file_out):
 
     sample_mapping_dict = {}
     with open(file_in, "r") as fin:
-
         ## Check header
         MIN_COLS = 2
         # TODO nf-core: Update the column names for the input samplesheet
         HEADER = ["sample", "fastq_1", "fastq_2"]
+        assembly_header = ["sample", "fna_file_path"]
         header = [x.strip('"') for x in fin.readline().strip().split(",")]
-        if header[: len(HEADER)] != HEADER:
-            print("ERROR: Please check samplesheet header -> {} != {}".format(",".join(header), ",".join(HEADER)))
+        if header[: len(assembly_header)] == assembly_header:
+            print(
+                "ERROR: Assembly samplesheet found. Try using -entry annotation or -entry assembly_qc"
+            )
+
+        elif header[: len(HEADER)] != HEADER:
+            print(
+                "ERROR: Please check samplesheet header -> {} != {}".format(
+                    ",".join(header), ",".join(HEADER)
+                )
+            )
             sys.exit(1)
 
         ## Check sample entries
@@ -78,7 +87,9 @@ def check_samplesheet(file_in, file_out):
             num_cols = len([x for x in lspl if x])
             if num_cols < MIN_COLS:
                 print_error(
-                    "Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
+                    "Invalid number of populated columns (minimum = {})!".format(
+                        MIN_COLS
+                    ),
                     "Line",
                     line,
                 )
@@ -126,13 +137,20 @@ def check_samplesheet(file_in, file_out):
         with open(file_out, "w") as fout:
             fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n")
             for sample in sorted(sample_mapping_dict.keys()):
-
                 ## Check that multiple runs of the same sample are of the same datatype
-                if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]):
-                    print_error("Multiple runs of a sample must be of the same datatype!", "Sample: {}".format(sample))
+                if not all(
+                    x[0] == sample_mapping_dict[sample][0][0]
+                    for x in sample_mapping_dict[sample]
+                ):
+                    print_error(
+                        "Multiple runs of a sample must be of the same datatype!",
+                        "Sample: {}".format(sample),
+                    )
 
                 for idx, val in enumerate(sample_mapping_dict[sample]):
-                    fout.write(",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n")
+                    fout.write(
+                        ",".join(["{}_T{}".format(sample, idx + 1)] + val) + "\n"
+                    )
     else:
         print_error("No entries to process!", "Samplesheet: {}".format(file_in))