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nf-core · Oct 31, 2023 · 75eb163 · 75eb163
1 parent 44d8cab
commit 75eb163
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Showing 3 changed files with 37 additions and 15 deletions.
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -158,8 +158,14 @@ def check_samplesheet(file_in, file_out):
             sample_type = ""
             if "sample_type" in header:
                 sample_type = lspl[colmap["sample_type"]]
-                if (sample_type not in SAMPLE_TYPES):
-                    print_error("Sample type {} is not supported! Please specify either {}".format(sample_type, " or ".join(SAMPLE_TYPES)), "Line", line)
+                if sample_type not in SAMPLE_TYPES:
+                    print_error(
+                        "Sample type {} is not supported! Please specify either {}".format(
+                            sample_type, " or ".join(SAMPLE_TYPES)
+                        ),
+                        "Line",
+                        line,
+                    )
 
             for fastq in fastq_list:
                 if fastq:
@@ -194,7 +200,21 @@ def check_samplesheet(file_in, file_out):
     ## Write validated samplesheet with appropriate columns
     if len(sample_mapping_dict) > 0:
         with open(file_out, "w") as fout:
-            fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2", "expected_cells", "seq_center" , "fastq_barcode", "sample_type"]) + "\n")
+            fout.write(
+                ",".join(
+                    [
+                        "sample",
+                        "single_end",
+                        "fastq_1",
+                        "fastq_2",
+                        "expected_cells",
+                        "seq_center",
+                        "fastq_barcode",
+                        "sample_type",
+                    ]
+                )
+                + "\n"
+            )
             for sample in sorted(sample_mapping_dict.keys()):
 
                 ## Check that multiple runs of the same sample are of the same datatype

diff --git a/bin/generate_config.py b/bin/generate_config.py
@@ -16,12 +16,12 @@
 
     config = open("config", "w")
     config.write("{\n")
-    config.write("\torganism: \"{}\"\n".format(args["fasta"].split(".")[0]))
-    config.write("\tgenome: [\"cellrangerarc_reference\"]\n")
-    config.write("\tinput_fasta: [\"{}\"]\n".format(args["fasta"]))
-    config.write("\tinput_gtf: [\"{}\"]\n".format(args["gtf"]))
-    config.write("\tinput_motifs: \"{}\"\n".format(args["motifs"]))
-    if(args["add"] != "none"):
+    config.write('\torganism: "{}"\n'.format(args["fasta"].split(".")[0]))
+    config.write('\tgenome: ["cellrangerarc_reference"]\n')
+    config.write('\tinput_fasta: ["{}"]\n'.format(args["fasta"]))
+    config.write('\tinput_gtf: ["{}"]\n'.format(args["gtf"]))
+    config.write('\tinput_motifs: "{}"\n'.format(args["motifs"]))
+    if args["add"] != "none":
         config.write(args["add"] + "\n")
     config.write("}")
     config.close()

diff --git a/bin/generate_lib_csv.py b/bin/generate_lib_csv.py
@@ -22,13 +22,15 @@
     lib_csv = open(args["out"], "w")
     lib_csv.write("fastqs,sample,library_type")
 
-    for i in range(0,len(sample_types)):
-        if (sample_names[i] in unique_samples_names):
-            unique_samples_names.remove(sample_names[i]) # this has to be done to account for different Lane files (e.g., L002)
-            if(sample_types[i] == "gex"):
-                lib_csv.write("\n{},{},{}".format(args["fastq_folder"], sample_names[i],"Gene Expression"))
+    for i in range(0, len(sample_types)):
+        if sample_names[i] in unique_samples_names:
+            unique_samples_names.remove(
+                sample_names[i]
+            )  # this has to be done to account for different Lane files (e.g., L002)
+            if sample_types[i] == "gex":
+                lib_csv.write("\n{},{},{}".format(args["fastq_folder"], sample_names[i], "Gene Expression"))
             else:
-                lib_csv.write("\n{},{},{}".format(args["fastq_folder"], sample_names[i],"Chromatin Accessibility"))
+                lib_csv.write("\n{},{},{}".format(args["fastq_folder"], sample_names[i], "Chromatin Accessibility"))
 
     lib_csv.close()