Updated README and bumped version to 1.0.4

README.md

@@ -51,6 +51,7 @@ optional arguments:
                         Space separated INPUT bam files (at least 2 files).
   --peak_beds PEAK_BEDS [PEAK_BEDS ...]
                         Space separated peak bed files (at least 2 files).
+  --ids IDS [IDS ...]   Optional space separated short IDs (e.g., S1, S2, S3) for datasets.
   --read_type READ_TYPE
                         Read type of eCLIP experiment, either SE or PE.
   --outdir OUTDIR       Path to output directory.

peak/peak.py

@@ -21,7 +21,7 @@
 parser.add_argument('--ip_bams', nargs='+', help='Space separated IP bam files (at least 2 files).')
 parser.add_argument('--input_bams', nargs='+', help='Space separated INPUT bam files (at least 2 files).')
 parser.add_argument('--peak_beds', nargs='+', help="Space separated peak bed files (at least 2 files).")
-parser.add_argument('--ids', nargs='+', help="Space separated short IDs (e.g., S1, S2, S3) for datasets.")
+parser.add_argument('--ids', nargs='+', help="Optional space separated short IDs (e.g., S1, S2, S3) for datasets.")
 parser.add_argument('--read_type', help="Read type of eCLIP experiment, either SE or PE.", default='PE')
 parser.add_argument('--outdir', type=str, help="Path to output directory.")
 parser.add_argument('--species', type=str, help="Short code for species, e.g., hg19, mm10.")

setup.py

@@ -17,7 +17,7 @@
 
 setup(
     name='eclip-peak',
-    version='1.0.3',
+    version='1.0.4',
     description='Pipeline for using IDR to identify a set of reproducible peaks given eClIP dataset with '
                 'two or three replicates.',
     long_description=long_description,