minor doc and WDL changes

broadinstitute · Jan 5, 2018 · 3ee825d · 3ee825d
1 parent 1d1a8d7
commit 3ee825d
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 13 deletions.
diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
@@ -33,7 +33,6 @@ workflow CNVGermlineCaseWorkflow {
     File ref_fasta_fai
     File ref_fasta
     String gatk_docker
-    Int? preemptible_attempts
 
     ##################################
     #### optional basic arguments ####
@@ -43,6 +42,7 @@ workflow CNVGermlineCaseWorkflow {
     Int? mem_for_germline_cnv_caller
     Int? cpu_for_determine_germline_contig_ploidy
     Int? cpu_for_germline_cnv_caller
+    Int? preemptible_attempts
 
     ###################################################
     #### optional arguments for ploidy case caller ####

diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -35,7 +35,6 @@ workflow CNVGermlineCohortWorkflow {
     File ref_fasta_fai
     File ref_fasta
     String gatk_docker
-    Int? preemptible_attempts
 
     ##################################
     #### optional basic arguments ####
@@ -45,6 +44,7 @@ workflow CNVGermlineCohortWorkflow {
     Int? mem_for_germline_cnv_caller
     Int? cpu_for_determine_germline_contig_ploidy
     Int? cpu_for_germline_cnv_caller
+    Int? preemptible_attempts
 
     #####################################################
     #### optional arguments for ploidy cohort caller ####

diff --git a/...in/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java b/...in/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java
@@ -28,7 +28,7 @@
 import java.util.stream.Collectors;
 
 /**
- * Determine the baseline contig ploidy for germline samples given counts data.
+ * Determines the baseline contig ploidy for germline samples given counts data.
  * These should be either HDF5 or TSV count files generated by {@link CollectFragmentCounts}.
  *
  * <p>
@@ -99,7 +99,7 @@
  *
  * <p>COHORT mode:</p>
  * <pre>
- * gatk --javaOptions "-Xmx4g" DetermineGermlineContigPloidy \
+ * gatk DetermineGermlineContigPloidy \
  *   --input normal_1.counts.hdf5 \
  *   --input normal_2.counts.hdf5 \
  *   ... \
@@ -110,7 +110,7 @@
  *
  * <p>CASE mode:</p>
  * <pre>
- * gatk --javaOptions "-Xmx4g" DetermineGermlineContigPloidy \
+ * gatk DetermineGermlineContigPloidy \
  *   --model a_valid_ploidy_model_dir
  *   --input normal_1.counts.hdf5 \
  *   --input normal_2.counts.hdf5 \
@@ -123,8 +123,8 @@
  * @author Samuel Lee &lt;[email protected]&gt;
  */
 @CommandLineProgramProperties(
-        summary = "Determine the baseline contig ploidy for germline samples given counts data.",
-        oneLineSummary = "Determine the baseline contig ploidy for germline samples given counts data.",
+        summary = "Determines the baseline contig ploidy for germline samples given counts data.",
+        oneLineSummary = "Determines the baseline contig ploidy for germline samples given counts data.",
         programGroup = CopyNumberProgramGroup.class
 )
 @DocumentedFeature

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java
@@ -30,7 +30,7 @@
 import java.util.stream.Collectors;
 
 /**
- * Call copy-number variants in germline samples given their counts and the corresponding output of
+ * Calls copy-number variants in germline samples given their counts and the corresponding output of
  * {@link DetermineGermlineContigPloidy}. The former should be either HDF5 or TSV count files generated by
  * {@link CollectFragmentCounts}.
  *
@@ -108,15 +108,15 @@
  *      the python subprocess. Generally speaking, the resource requirements of this tool scale linearly with each of the
  *      number of samples, the number of modeled intervals, the highest copy number state, the number of bias factors, and
  *      the number of knobs on the GC curve. For example, the python subprocess requires approximately 16gb for RAM for
- *      modeling 10'000 intervals for 100 samples, with 16 maximum bias factors and explicit GC bias modeling.
+ *      modeling 10000 intervals for 100 samples, with 16 maximum bias factors and explicit GC bias modeling.
  *     </p></dd>
  * </dl>
  *
  * <h3>Usage examples</h3>
  *
  * <p>COHORT mode:</p>
  * <pre>
- * gatk --javaOptions "-Xmx4g" GermlineCNVCaller \
+ * gatk GermlineCNVCaller \
  *   --run-mode COHORT \
  *   -L intervals.interval_list \
  *   --contig-ploidy-calls path_to_contig_ploidy_calls
@@ -129,7 +129,7 @@
  *
  * <p>CASE mode:</p>
  * <pre>
- * gatk --javaOptions "-Xmx4g" GermlineCNVCaller \
+ * gatk GermlineCNVCaller \
  *   --run-mode CASE \
  *   -L intervals.interval_list \
  *   --contig-ploidy-calls path_to_contig_ploidy_calls
@@ -144,9 +144,9 @@
  * @author Samuel Lee &lt;[email protected]&gt;
  */
 @CommandLineProgramProperties(
-        summary = "Denoise and call copy-number variants in germline samples given their counts and " +
+        summary = "Calls copy-number variants in germline samples given their counts and " +
                 "the output of DetermineGermlineContigPloidy.",
-        oneLineSummary = "Denoise and call copy-number variants in germline samples given their counts and " +
+        oneLineSummary = "Calls copy-number variants in germline samples given their counts and " +
                 "the output of DetermineGermlineContigPloidy.",
         programGroup = CopyNumberProgramGroup.class
 )