diff options
| -rw-r--r-- | tools/gridss-assemble.nix | 3 | ||||
| -rw-r--r-- | tools/gridss-collectMetrics.nix | 9 | ||||
| -rw-r--r-- | tools/gridss-extractSVReads.nix | 3 | ||||
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 9 | ||||
| -rw-r--r-- | tools/gridss-variants.nix | 3 |
5 files changed, 15 insertions, 12 deletions
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index 14f39c8..a532f4b 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -55,7 +55,8 @@ stage rec { OUTPUT=$out \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ WORKING_DIR=$TMPDIR/ \ - TMP_DIR=$TMPDIR/ + TMP_DIR=$TMPDIR/ \ + ${optionalString (flags != null) flags} ''; passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; }; passthru.multicore = true; diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix index 2e3b3a9..8b09886 100644 --- a/tools/gridss-collectMetrics.nix +++ b/tools/gridss-collectMetrics.nix @@ -22,13 +22,14 @@ stage rec { buildCommand = '' mkdir $out java -Xmx${heapSize} -cp ${bionix.gridss.jar} \ - gridss.analysis.CollectGridssMetrics \ + gridss.analysis.CollectGridssMetrics \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ VERBOSITY=WARNING \ - I=${input}\ - O=$out/input \ + I=${input}\ + O=$out/input \ AS=true \ - THRESHOLD_COVERAGE=${toString thresholdCoverage} + THRESHOLD_COVERAGE=${toString thresholdCoverage} \ + ${optionalString (flags != null) flags} # Make the output deterministic by removing timestamps sed -i '/^# Started on:/d' $out/input.*_metrics diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix index cf9085d..6691808 100644 --- a/tools/gridss-extractSVReads.nix +++ b/tools/gridss-extractSVReads.nix @@ -38,7 +38,8 @@ stage rec { O=$out \ UNMAPPED_READS=${if unmappedReads then "true" else "false"} \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ - MIN_CLIP_LENGTH=${toString minClipLength} + MIN_CLIP_LENGTH=${toString minClipLength} \ + ${optionalString (flags != null) flags} ''; passthru.filetype = input.filetype; } diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index d480328..93d02df 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -30,12 +30,13 @@ stage rec { java -Xmx${heapSize} -Dsamjdk.create_index=false \ -cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \ VERBOSITY=WARNING \ - REFERENCE_SEQUENCE=ref.fa \ - I=${input} \ - O=$out \ + REFERENCE_SEQUENCE=ref.fa \ + I=${input} \ + O=$out \ ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ - WORKER_THREADS=$NIX_BUILD_CORES + WORKER_THREADS=$NIX_BUILD_CORES \ + ${optionalString (flags != null) flags} ''; passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; }; passthru.multicore = true; diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index 4f39b1e..ad4c66d 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -5,7 +5,6 @@ , assemblyAttrs ? {} , collectMetricsAttrs ? {} , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } -, flags ? null , config ? null , heapSize ? "4g" }: @@ -91,7 +90,7 @@ rec { name = "gridss-annotateVariants"; buildInputs = with pkgs; [ jre ]; buildCommand = mkLinks + '' - ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf + ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs config; } inputs} input.vcf java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.AnnotateVariants \ VERBOSITY=WARNING \ |