diff options
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | tools/bwa-index.nix | 2 | ||||
| -rw-r--r-- | tools/bwa-mem.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-callVariants.nix | 2 | ||||
| -rw-r--r-- | tools/platypus-callVariants.nix | 2 | ||||
| -rw-r--r-- | tools/samtools-faidx.nix | 1 | ||||
| -rw-r--r-- | tools/strelka-call.nix | 4 |
7 files changed, 8 insertions, 7 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index f8c49ec..3260b7b 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -14,7 +14,7 @@ in with bionix; let - ref = ./example/ref.fa; + ref = { seq = ./example/ref.fa; }; alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; sort = samtools.sort {}; flagstat = samtools.flagstat {}; diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix index 3f9d385..48a2556 100644 --- a/tools/bwa-index.nix +++ b/tools/bwa-index.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation { name = "bwa-index"; buildInputs = [ bwa ]; buildCommand = '' - ln -s ${ref} ref.fa + ln -s ${ref.seq} ref.fa bwa index ${optionalString (flags != null) flags} ref.fa mkdir $out mv ref.fa.* $out diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index 6e83a6d..ca9e6a8 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation { name = "bwa-mem"; buildInputs = [ bwa bc ] ++ optional bamOutput samtools; buildCommand = '' - ln -s ${ref} ref.fa + ln -s ${ref.seq} ref.fa for f in ${bionix.bwa.index indexAttrs ref}/* ; do ln -s $f done diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index e431560..c313c3f 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; }; buildCommand = '' - ln -s ${ref} ref.fa + ln -s ${ref.seq} ref.fa ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do ln -s $f diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix index c0204dc..7b68b28 100644 --- a/tools/platypus-callVariants.nix +++ b/tools/platypus-callVariants.nix @@ -16,7 +16,7 @@ in stdenv.mkDerivation { name = "platypus"; buildInputs = [ platypus ]; buildCommand = '' - ln -s ${ref} ref.fa + ln -s ${ref.seq} ref.fa ln -s ${bionix.samtools.faix indexAttrs ref} ref.fa.fai ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs} diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix index 72116b8..bf32bdf 100644 --- a/tools/samtools-faidx.nix +++ b/tools/samtools-faidx.nix @@ -9,6 +9,7 @@ with nixpkgs; with lib; stdenv.mkDerivation { + name = "samtools-faidx"; buildInputs = [ samtools ]; buildCommand = '' diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix index e7fbb58..ecdea84 100644 --- a/tools/strelka-call.nix +++ b/tools/strelka-call.nix @@ -19,8 +19,8 @@ in stdenv.mkDerivation { name = "strelka"; buildInputs = [ strelka ]; buildCommand = '' - ln -s ${ref} ref.fa - ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai + ln -s ${ref.seq} ref.fa + ln -s ${bionix.samtools.faidx indexAttrs ref.seq} ref.fa.fai ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs} |