diff options
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 9 |
1 files changed, 9 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 31570ee..ef2af1b 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -6,6 +6,8 @@ let ref = ./example/ref.fa; alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; sort = samtools.sort { }; + flagstat = samtools.flagstat {}; + check = fastqc.check {}; callVariants = strelka.call { inherit ref; }; tnpair = { tumour = {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};}; @@ -26,6 +28,13 @@ let mkdir $out/alignments ln -s ${tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.bam ln -s ${tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.bam + ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat + ln -s ${flagstat tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.flagstat + mkdir $out/fastqc + ln -s ${check tnpair.tumour.files.input1} $out/fastqc/${tnpair.tumour.name}.1 + ln -s ${check tnpair.tumour.files.input2} $out/fastqc/${tnpair.tumour.name}.2 + ln -s ${check tnpair.normal.files.input1} $out/fastqc/${tnpair.normal.name}.1 + ln -s ${check tnpair.normal.files.input2} $out/fastqc/${tnpair.normal.name}.2 ''; }; |