diff options
| author | Justin Bedo <cu@cua0.org> | 2019-03-28 13:40:31 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-28 13:40:31 +1100 |
| commit | dbbfc5655b840e9cd1d10993b411376ec0a90135 (patch) | |
| tree | 17f3a63cd9ab7c6407eeb6b88ffe0488b9932deb | |
| parent | 1d01a7faf089bc4ce221a4460abf613dd279e2a7 (diff) | |
gridss: less chatty logs
| -rw-r--r-- | tools/gridss-assemble.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-callVariants.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-collectMetrics.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-computeSamTags.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-extractSVReads.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 1 | ||||
| -rw-r--r-- | tools/gridss-variants.nix | 2 |
7 files changed, 8 insertions, 0 deletions
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index 27bbe32..14f39c8 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -48,6 +48,7 @@ stage rec { ${concatMapStringsSep "\n" linkInput inputs} java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${bionix.gridss.jar} gridss.AssembleBreakends \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ WORKER_THREADS=$NIX_BUILD_CORES \ diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index 1ec9206..ffbb349 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -39,6 +39,7 @@ stage rec { -Dsamjdk.use_async_io_write_tribble=true \ -Dgridss.gridss.output_to_temp_file=true \ -cp ${bionix.gridss.jar} gridss.CallVariants \ + VERBOSITY=WARNING \ WORKER_THREADS=$NIX_BUILD_CORES \ TMP_DIR=. \ WORKING_DIR=. \ diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix index 37e22f1..c62346e 100644 --- a/tools/gridss-collectMetrics.nix +++ b/tools/gridss-collectMetrics.nix @@ -24,6 +24,7 @@ stage rec { java -Xmx${heapSize} -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ + VERBOSITY=WARNING \ I=${input}\ O=$out/input \ AS=true \ diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix index 5e35749..a2e1f8b 100644 --- a/tools/gridss-computeSamTags.nix +++ b/tools/gridss-computeSamTags.nix @@ -31,6 +31,7 @@ stage rec { java -Xmx${heapSize} \ -Dsamjdk.create_index=false \ -cp ${bionix.gridss.jar} gridss.ComputeSamTags \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ WORKING_DIR=$TMP_DIR \ TMP_DIR=$TMP_DIR \ diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix index f2fab30..cf9085d 100644 --- a/tools/gridss-extractSVReads.nix +++ b/tools/gridss-extractSVReads.nix @@ -32,6 +32,7 @@ stage rec { done java -Dsamjdk.create_index=true \ -cp ${bionix.gridss.jar} gridss.ExtractSVReads \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ I=input.bam \ O=$out \ diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 4a73e3c..d480328 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -29,6 +29,7 @@ stage rec { done java -Xmx${heapSize} -Dsamjdk.create_index=false \ -cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ I=${input} \ O=$out \ diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index fc26c5a..b564725 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -70,6 +70,7 @@ rec { buildCommand = mkLinks + '' java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.IdentifyVariants \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ @@ -93,6 +94,7 @@ rec { ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.AnnotateVariants \ + VERBOSITY=WARNING \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ |