Expanded WDL documentation.

scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl

@@ -2,10 +2,17 @@
 #
 # Notes:
 #
-# - The interval-list file is required for both WGS and WES workflows and should be a Picard or GATK-style interval list.
+# - The intervals argument is required for both WGS and WES workflows and accepts formats compatible with the
+#   GATK -L argument (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
 #   These intervals will be padded on both sides by the amount specified by PreprocessIntervals.padding (default 250)
-#   and split into bins of length specified by PreprocessIntervals.bin_length (default 1000; specify 0 to skip binning).
-#   For WGS, the intervals should simply cover the chromosomes of interest.
+#   and split into bins of length specified by PreprocessIntervals.bin_length (default 1000; specify 0 to skip binning,
+#   e.g., for WES).  For WGS, the intervals should simply cover the chromosomes of interest.
+#
+# - Intervals can be blacklisted from coverage collection and all downstream steps by using the blacklist_intervals
+#   argument, which accepts formats compatible with the GATK -XL argument
+#   (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
+#   This may be useful for excluding centromeric regions, etc. from analysis.  Alternatively, these regions may
+#   be manually filtered from the final callset.
 #
 # - Example invocation:
 #

scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl

@@ -2,10 +2,17 @@
 #
 # Notes:
 #
-# - The interval-list file is required for both WGS and WES workflows and should be a Picard or GATK-style interval list.
+# - The intervals argument is required for both WGS and WES workflows and accepts formats compatible with the
+#   GATK -L argument (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
 #   These intervals will be padded on both sides by the amount specified by PreprocessIntervals.padding (default 250)
-#   and split into bins of length specified by PreprocessIntervals.bin_length (default 1000; specify 0 to skip binning).
-#   For WGS, the intervals should simply cover the chromosomes of interest.
+#   and split into bins of length specified by PreprocessIntervals.bin_length (default 1000; specify 0 to skip binning,
+#   e.g., for WES).  For WGS, the intervals should simply cover the chromosomes of interest.
+#
+# - Intervals can be blacklisted from coverage collection and all downstream steps by using the blacklist_intervals
+#   argument, which accepts formats compatible with the GATK -XL argument
+#   (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
+#   This may be useful for excluding centromeric regions, etc. from analysis.  Alternatively, these regions may
+#   be manually filtered from the final callset.
 #
 # - Example invocation:
 #

scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl

@@ -2,13 +2,20 @@
 #
 # Notes:
 #
-# - The interval-list file is required for both WGS and WES workflows and should be a Picard or GATK-style interval list.
+# - The intervals argument is required for both WGS and WES workflows and accepts formats compatible with the
+#   GATK -L argument (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
 #   These intervals will be padded on both sides by the amount specified by PreprocessIntervals.padding (default 250)
 #   and split into bins of length specified by PreprocessIntervals.bin_length (default 1000; specify 0 to skip binning,
-#   e.g. for WES).  For WGS, the intervals should simply cover the autosomal chromosomes (sex chromosomes may be
+#   e.g., for WES).  For WGS, the intervals should simply cover the autosomal chromosomes (sex chromosomes may be
 #   included, but care should be taken to 1) avoid creating panels of mixed sex, and 2) denoise case samples only
 #   with panels containing only individuals of the same sex as the case samples).
 #
+# - Intervals can be blacklisted from coverage collection and all downstream steps by using the blacklist_intervals
+#   argument, which accepts formats compatible with the GATK -XL argument
+#   (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
+#   This may be useful for excluding centromeric regions, etc. from analysis.  Alternatively, these regions may
+#   be manually filtered from the final callset.
+#
 # - The sites file (common_sites) should be a Picard or GATK-style interval list.  This is a list of sites
 #   of known variation at which allelic counts will be collected for use in modeling minor-allele fractions.
 #

scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl

@@ -2,13 +2,20 @@
 #
 # Notes:
 #
-# - The interval-list file is required for both WGS and WES workflows and should be a Picard or GATK-style interval list.
+# - The intervals argument is required for both WGS and WES workflows and accepts formats compatible with the
+#   GATK -L argument (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
 #   These intervals will be padded on both sides by the amount specified by PreprocessIntervals.padding (default 250)
 #   and split into bins of length specified by PreprocessIntervals.bin_length (default 1000; specify 0 to skip binning,
-#   e.g. for WES).  For WGS, the intervals should simply cover the autosomal chromosomes (sex chromosomes may be
+#   e.g., for WES).  For WGS, the intervals should simply cover the autosomal chromosomes (sex chromosomes may be
 #   included, but care should be taken to 1) avoid creating panels of mixed sex, and 2) denoise case samples only
 #   with panels containing only individuals of the same sex as the case samples).
 #
+# - Intervals can be blacklisted from coverage collection and all downstream steps by using the blacklist_intervals
+#   argument, which accepts formats compatible with the GATK -XL argument
+#   (see https://gatkforums.broadinstitute.org/gatk/discussion/11009/intervals-and-interval-lists).
+#   This may be useful for excluding centromeric regions, etc. from analysis.  Alternatively, these regions may
+#   be manually filtered from the final callset.
+#
 # - Example invocation:
 #
 #       java -jar cromwell.jar run cnv_somatic_panel_workflow.wdl -i my_parameters.json