Merge pull request #29 from Sage-Bionetworks-Workflows/bwmac/ORCA-189/support_fastq

[ORCA-189] Adds support for FASTQ and FASTQ-GZ files

Author: BWMac

src/dcqc/file.py

@@ -109,6 +109,7 @@ def get_file_type(cls, file_type: str) -> FileType:
 FileType("OME-TIFF", (".ome.tif", ".ome.tiff"), "format_3727")
 FileType("TSV", (".tsv"), "format_3475")
 FileType("BAM", (".bam"), "format_2572")
+FileType("FASTQ", (".fastq", ".fastq.gz", ".fq", ".fq.gz"), "format_1930")
 
 
 # TODO: Leverage post-init function in dataclasses

src/dcqc/suites/suites.py

@@ -36,3 +36,7 @@ class TSVSuite(FileSuite):
 
 class BAMSuite(FileSuite):
     file_type = FileType.get_file_type("BAM")
+
+
+class FastqSuite(FileSuite):
+    file_type = FileType.get_file_type("FASTQ")

tests/data/example.fastq

@@ -0,0 +1 @@
+foobar

tests/data/example.fastq.gz

@@ -0,0 +1 @@
+foobar

tests/data/files.csv

@@ -7,3 +7,5 @@ circuit.tif,TIFF,c7b08f6decb5e7572efbe6074926a843
 example.jsonld,JSON-LD,56bb5f34da6d6df2ade3ac37e25586b7
 example.tsv,TSV,f47c75614087a8dd938ba4acff252494
 example.bam,BAM,14758f1afd44c09b7992073ccf00b43d
+example.fastq,FASTQ,14758f1afd44c09b7992073ccf00b43d
+example.fastq.gz,FASTQ,14758f1afd44c09b7992073ccf00b43d