diff options
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-assemble.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-callVariants.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-collectGridssMetrics.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-collectMetrics.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-computeSamTags.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-extractSVReads.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-identifyVariants.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 2 |
9 files changed, 9 insertions, 9 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix index adc4958..655b268 100644 --- a/tools/gridss-annotateVariants.nix +++ b/tools/gridss-annotateVariants.nix @@ -73,7 +73,7 @@ stdenv.mkDerivation rec { INPUT_VCF=input.vcf \ OUTPUT_VCF=out.vcf \ WORKING_DIR=$TMPDIR/ \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ TMP_DIR=$TMPDIR/ mv out.vcf $out diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index b61f28a..847830a 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -51,7 +51,7 @@ stdenv.mkDerivation rec { ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ WORKER_THREADS=$NIX_BUILD_CORES \ OUTPUT=$out \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ ''; diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index 76adc74..48f7cb2 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { WORKER_THREADS=$NIX_BUILD_CORES \ TMP_DIR=. \ WORKING_DIR=. \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ REFERENCE_SEQUENCE="ref.fa" \ ${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \ OUTPUT="$out/gridss.vcf" \ diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix index 3babab4..91e04c7 100644 --- a/tools/gridss-collectGridssMetrics.nix +++ b/tools/gridss-collectGridssMetrics.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { java -Xmx1G -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ ${optionalString sorted "ASSUME_SORTED=true"} \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ I=input.bam \ O=$out \ THRESHOLD_COVERAGE=${toString thresholdCoverage} diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix index ff6eb1f..b68aeb1 100644 --- a/tools/gridss-collectMetrics.nix +++ b/tools/gridss-collectMetrics.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { mkdir $out java -Xmx1G -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ I=${input}\ O=$out/input \ AS=true \ diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix index f4f1617..9267809 100644 --- a/tools/gridss-computeSamTags.nix +++ b/tools/gridss-computeSamTags.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { REFERENCE_SEQUENCE=ref.fa \ WORKING_DIR=$TMP_DIR \ TMP_DIR=$TMP_DIR \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ I=${input} \ O=$out \ AS=true diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix index b50a01c..5fc4c59 100644 --- a/tools/gridss-extractSVReads.nix +++ b/tools/gridss-extractSVReads.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { I=input.bam \ O=$out \ UNMAPPED_READS=${if unmappedReads then "true" else "false"} \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ MIN_CLIP_LENGTH=${toString minClipLength} ''; passthru.filetype = input.filetype; diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix index d2dc665..23a9d85 100644 --- a/tools/gridss-identifyVariants.nix +++ b/tools/gridss-identifyVariants.nix @@ -69,7 +69,7 @@ stdenv.mkDerivation rec { ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ OUTPUT_VCF=out.vcf \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 2fff15c..9bce063 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { I=${input} \ O=$out \ ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ + ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ WORKER_THREADS=$NIX_BUILD_CORES ''; passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;}; |