From dab5de1990ca18edb79bd11fc92a2ed6551a4ead Mon Sep 17 00:00:00 2001 From: Chris Saunders Date: Tue, 9 Jun 2015 16:52:18 -0700 Subject: [PATCH] docs: clarify that input is currently BAM-only --- src/python/bin/configManta.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/python/bin/configManta.py b/src/python/bin/configManta.py index 582153e6..9e2c6ebb 100644 --- a/src/python/bin/configManta.py +++ b/src/python/bin/configManta.py @@ -38,15 +38,15 @@ def workflowDescription(self) : return """Version: %s This script configures the Manta SV analysis pipeline. -You must specify a BAM or CRAM file for at least one sample. +You must specify a BAM file for at least one sample. """ % (workflowVersion) def addWorkflowGroupOptions(self,group) : group.add_option("--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append", - help="Normal sample BAM or CRAM file. May be specified more than once, multiple inputs will be merged. [at least one required] (no default)") + help="Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [at least one required] (no default)") group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append", - help="Tumor sample BAM or CRAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)") + help="Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)") group.add_option("--exome", dest="isExome", action="store_true", help="Set options for WES input: turn off depth filters") group.add_option("--rna", dest="isRNA", action="store_true",