diff options
| -rw-r--r-- | tools/gridss-annotateVariants.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 | ||||
| -rw-r--r-- | tools/gridss.nix | 1 |
9 files changed, 17 insertions, 0 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix index 4f66c6c..33992c4 100644 --- a/tools/gridss-annotateVariants.nix +++ b/tools/gridss-annotateVariants.nix @@ -8,6 +8,7 @@ , softClipsToSplitReadsAttrs ? {} , identifyVariantsAttrs ? {} , flags ? null +, config ? null }: with nixpkgs; @@ -64,6 +65,7 @@ stdenv.mkDerivation rec { INPUT_VCF=input.vcf \ OUTPUT_VCF=out.vcf \ WORKING_DIR=$TMPDIR/ \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ TMP_DIR=$TMPDIR/ mv out.vcf $out diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index 416eb7c..dc978fa 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -4,6 +4,7 @@ , bwaIndexAttrs ? {} , faidxAttrs ? {} , flags ? null +, config ? null }: with nixpkgs; @@ -41,6 +42,7 @@ stdenv.mkDerivation rec { WORKER_THREADS=$NIX_BUILD_CORES \ TMP_DIR=. \ WORKING_DIR=. \ + ${optionalString config ("CONFIGURATION_FILE=" + 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 bb8d2e9..86732b8 100644 --- a/tools/gridss-collectGridssMetrics.nix +++ b/tools/gridss-collectGridssMetrics.nix @@ -2,6 +2,7 @@ , nixpkgs , thresholdCoverage ? 10000 , flags ? null +, config ? null }: with nixpkgs; @@ -25,6 +26,7 @@ stdenv.mkDerivation rec { java -Xmx1G -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ ${optionalString sorted "ASSUME_SORTED=true"} \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ I=input.bam \ O=$out \ THRESHOLD_COVERAGE=${toString thresholdCoverage} diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix index 4688808..c1909f1 100644 --- a/tools/gridss-collectMetrics.nix +++ b/tools/gridss-collectMetrics.nix @@ -2,6 +2,7 @@ , nixpkgs , thresholdCoverage ? 10000 , flags ? null +, config ? null }: with nixpkgs; @@ -22,6 +23,7 @@ stdenv.mkDerivation rec { mkdir $out java -Xmx1G -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ I=${input}\ O=$out/input \ AS=true \ diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix index f75cea0..5b19a3a 100644 --- a/tools/gridss-computeSamTags.nix +++ b/tools/gridss-computeSamTags.nix @@ -4,6 +4,7 @@ , bwaIndexAttrs ? {} , faidxAttrs ? {} , flags ? null +, config ? null }: with nixpkgs; @@ -34,6 +35,7 @@ stdenv.mkDerivation rec { REFERENCE_SEQUENCE=ref.fa \ WORKING_DIR=$TMP_DIR \ TMP_DIR=$TMP_DIR \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ I=${input} \ O=$out \ AS=true diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix index a10abf5..e3ed1cc 100644 --- a/tools/gridss-extractSVReads.nix +++ b/tools/gridss-extractSVReads.nix @@ -5,6 +5,7 @@ , flags ? null , unmappedReads ? false , minClipLength ? 5 +, config ? null }: with nixpkgs; @@ -35,6 +36,7 @@ stdenv.mkDerivation rec { METRICS_OUTPUT=$out/input.sv_metrics \ INSERT_SIZE_METRICS=$out/input.insert_size_metrics \ UNMAPPED_READS=${if unmappedReads then "true" else "false"} \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ MIN_CLIP_LENGTH=${toString minClipLength} ''; } diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix index f44771b..16982e2 100644 --- a/tools/gridss-identifyVariants.nix +++ b/tools/gridss-identifyVariants.nix @@ -7,6 +7,7 @@ , collectMetricsAttrs ? {} , softClipsToSplitReadsAttrs ? {} , flags ? null +, config ? null }: with nixpkgs; @@ -60,6 +61,7 @@ stdenv.mkDerivation rec { ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ ASSEMBLY=${assembly} \ OUTPUT_VCF=out.vcf \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 8a7dca3..35cd7b4 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -4,6 +4,7 @@ , faidxAttrs ? {} , alignerStreaming ? false , flags ? null +, config ? null }: with nixpkgs; @@ -33,6 +34,7 @@ stdenv.mkDerivation rec { I=${input} \ O=$out \ ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ WORKER_THREADS=$NIX_BUILD_CORES ''; passthru.filetype = diff --git a/tools/gridss.nix b/tools/gridss.nix index d46a8ce..bc2f0b8 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -8,6 +8,7 @@ rec { url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar"; sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; }; + gridssConfig = callBionix ./gridss-configFile.nix {}; callVariants = callBionix ./gridss-callVariants.nix; computeSamTags = callBionix ./gridss-computeSamTags.nix; softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix; |