Support uncompressed FASTQ file formats (.fastq, .fq)

bin/check_samplesheet.py

@@ -3,6 +3,7 @@
 """
 adapted from: https://github.com/nf-core/chipseq/blob/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/bin/check_samplesheet.py
 """
+
 import collections
 import os
 import errno
@@ -106,9 +107,14 @@ def check_samplesheet(file_in, file_out):
                 if fastq:
                     if fastq.find(" ") != -1:
                         print_error("FastQ file contains spaces!", "Line", line)
-                    if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"):
+                    if not (
+                        fastq.endswith(".fastq.gz")
+                        or fastq.endswith(".fq.gz")
+                        or fastq.endswith(".fastq")
+                        or fastq.endswith(".fq")
+                    ):
                         print_error(
-                            "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!",
+                            "FastQ file does not have extension '.fastq.gz', '.fq.gz', '.fastq', or '.fq'!",
                             "Line",
                             line,
                         )

docs/guide/usage.md

@@ -76,8 +76,8 @@ The following columns are required:
 
 - `sample`: sample ID; does not need to be a unique column.
 - `rep`: replicate number of sample ID; does not need to be a unique column.
-- `fastq_1`: absolute path to R1 of sample ID.
-- `fastq_2`: absolute path to R2 of sample ID (optional, only for paired-end reads).
+- `fastq_1`: absolute path to R1 of sample ID. Files can be in compressed (`.fastq.gz`, `.fq.gz`) or uncompressed (`.fastq`, `.fq`) format.
+- `fastq_2`: absolute path to R2 of sample ID (optional, only for paired-end reads). Files can be in compressed (`.fastq.gz`, `.fq.gz`) or uncompressed (`.fastq`, `.fq`) format.
 - `antibody`: name of the antibody used for the sample.
 - `input`: the sampleID of the input control; this must match a sample in the sheet.