diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 1 | ||||
| -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-configFile.nix | 4 | ||||
| -rw-r--r-- | tools/gridss-extractSVReads.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-identifyVariants.nix | 2 |
11 files changed, 12 insertions, 10 deletions
@@ -1,2 +1,3 @@ result .DS_Store +.#* diff --git a/test-tnpair.nix b/test-tnpair.nix index a6ea163..0f6a441 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -54,7 +54,6 @@ let ln -s ${tnpairResult.variants} $out/strelka mkdir $out/alignments ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss - ln -s ${gridss.call (with tnpairResult.alignments; [tumour])} $out/gridss2 ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix index cae5daf..122c451 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=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ TMP_DIR=$TMPDIR/ mv out.vcf $out diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index 1bda91f..9afb213 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -5,6 +5,7 @@ , indexAttrs ? {} , collectMetricsAttrs ? {} , flags ? null +, config ? null }: with nixpkgs; @@ -50,6 +51,7 @@ stdenv.mkDerivation rec { ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ WORKER_THREADS=$NIX_BUILD_CORES \ OUTPUT=$out \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ ''; diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index 9afaf65..76adc74 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { WORKER_THREADS=$NIX_BUILD_CORES \ TMP_DIR=. \ WORKING_DIR=. \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_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 86732b8..3babab4 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 ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ I=input.bam \ O=$out \ THRESHOLD_COVERAGE=${toString thresholdCoverage} diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix index 38bacc6..ff6eb1f 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=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ I=${input}\ O=$out/input \ AS=true \ diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix index ebcc5b8..f4f1617 100644 --- a/tools/gridss-computeSamTags.nix +++ b/tools/gridss-computeSamTags.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { REFERENCE_SEQUENCE=ref.fa \ WORKING_DIR=$TMP_DIR \ TMP_DIR=$TMP_DIR \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ I=${input} \ O=$out \ AS=true diff --git a/tools/gridss-configFile.nix b/tools/gridss-configFile.nix index 838c292..15eba55 100644 --- a/tools/gridss-configFile.nix +++ b/tools/gridss-configFile.nix @@ -27,10 +27,10 @@ let builtins.head ( builtins.match "([0-9]+\.0?[1-9]*)0+" (builtins.toString attr))); bool = name: attr: name + " = " + (if attr == true then "true" else "false"); - attrs = name: attr: attrsToGridssConfigStringPrepend (name + ".") attr; + set = name: attr: attrsToGridssConfigStringPrepend (name + ".") attr; # Allows for repeated fields (e.g. for adapters): list = name: attr: concatStringsSep "\n" (map (x: iniLine name x) attr); }; in configAttrs: (writeText "gridss.properties.override" - (attrsToGridssConfigString configAttrs)) + ((attrsToGridssConfigString configAttrs) + "\n")) diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix index d260086..b50a01c 100644 --- a/tools/gridss-extractSVReads.nix +++ b/tools/gridss-extractSVReads.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { I=input.bam \ O=$out \ UNMAPPED_READS=${if unmappedReads then "true" else "false"} \ - ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ MIN_CLIP_LENGTH=${toString minClipLength} ''; passthru.filetype = input.filetype; diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix index d37e7ae..e5c74a4 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=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ |