diff options
| -rw-r--r-- | default.nix | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 12 | ||||
| -rw-r--r-- | tools/fastp-app.nix | 23 | ||||
| -rw-r--r-- | tools/fastp-run.nix | 40 | ||||
| -rw-r--r-- | tools/fastp.nix | 9 |
5 files changed, 80 insertions, 5 deletions
diff --git a/default.nix b/default.nix index 608fa9b..d67f2eb 100644 --- a/default.nix +++ b/default.nix @@ -33,6 +33,7 @@ let snpeff = callBionix ./tools/snpeff.nix {}; strelka = callBionix ./tools/strelka.nix {}; ascat = callBionix ./tools/ascat.nix {}; + fastp = callBionix ./tools/fastp.nix {}; sbatch = attrs: bionix.extend (self: super: with self; rec { sbatchDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; } // attrs; diff --git a/test-tnpair.nix b/test-tnpair.nix index 1d281fa..1b5f347 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -14,7 +14,8 @@ let alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; sort = samtools.sort {}; flagstat = samtools.flagstat {}; - check = fastqc.check {}; + check-fastqc = fastqc.check {}; + check-fastp = fastp.run {}; callVariants = strelka.callSomatic {}; markdup = samtools.markdup {}; fixmate = samtools.fixmate {}; @@ -59,10 +60,11 @@ let #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram") (ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat") #(ln (flagstat tnpairResult.alignments.normal) "alignments/${tnpair.normal.name}.flagstat") - (ln (check tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1") - #(ln (check tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2") - #(ln (check tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1") - #(ln (check tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2") + (ln (check-fastqc tnpair.tumour.files.input1) "fastqc/${tnpair.tumour.name}.1") + #(ln (check-fastqc tnpair.normal.files.input1) "fastqc/${tnpair.normal.name}.1") + #(ln (check-fastqc tnpair.normal.files.input2) "fastqc/${tnpair.normal.name}.2") + #(ln (check-fastqc tnpair.tumour.files.input2) "fastqc/${tnpair.tumour.name}.2") + (ln (check-fastp tnpair.tumour.files) "fastp/${tnpair.tumour.name}") ]; in testNaming diff --git a/tools/fastp-app.nix b/tools/fastp-app.nix new file mode 100644 index 0000000..bb716e2 --- /dev/null +++ b/tools/fastp-app.nix @@ -0,0 +1,23 @@ +{ stdenv +, fetchFromGitHub +, zlib +}: + +stdenv.mkDerivation rec { + name = "fastp-${version}"; + version = "0.20.0"; + + src = fetchFromGitHub { + owner = "OpenGene"; + repo = "fastp"; + rev = "v${version}"; + sha256 = "0y0qfp3j3gqnmlqskna8x43acss21vxwck287c4fagxlcaba0s30"; + }; + + buildInputs = [ zlib ]; + + installPhase = '' + mkdir -p $out/bin + cp fastp $out/bin + ''; +} diff --git a/tools/fastp-run.nix b/tools/fastp-run.nix new file mode 100644 index 0000000..c7cbb3c --- /dev/null +++ b/tools/fastp-run.nix @@ -0,0 +1,40 @@ +{ bionix +, flags ? null +} : + +{ input1 +, input2 ? null +} : + +with bionix; +with pkgs.lib; + +# Match input file type—how to do .fq and .fq.gz? Does bz2 work? + +stage { + name = "fastp"; + buildInputs = [ fastp.app ]; + outputs = [ "out" "fastq1" "fastq2" "html" "json" ]; + buildCommand = '' + mkdir -p $out + fastp \ + ${optionalString (flags != null) flags} \ + -i ${input1} \ + -o fastq1.fq.gz \ + ${optionalString (input2 != null) '' + -I ${input2} \ + -O fastq2.fq.gz \ + + cp fastq2.fq.gz $fastq2 + ln -s $fastq2 $out/fastq2.fq.gz + ''} + + cp fastq1.fq.gz $fastq1 + cp fastp.html $html + cp fastp.json $json + + ln -s $fastq1 $out/fastq1.fq.gz + ln -s $html $out/fastp.html + ln -s $json $out/fastp.json + ''; +}
\ No newline at end of file diff --git a/tools/fastp.nix b/tools/fastp.nix new file mode 100644 index 0000000..52c9041 --- /dev/null +++ b/tools/fastp.nix @@ -0,0 +1,9 @@ +{ bionix }: + +with bionix; + +rec { + app = pkgs.callPackage ./fastp-app.nix {}; + run = callBionixE ./fastp-run.nix; +} + |