diff options
Diffstat (limited to 'example')
-rw-r--r-- | example/call.nix | 19 | ||||
-rw-r--r-- | example/default.nix | 42 | ||||
-rw-r--r-- | example/ref.fa | 81302 | ||||
-rw-r--r-- | example/sample1-1.fq | 4000 | ||||
-rw-r--r-- | example/sample1-2.fq | 4000 | ||||
-rw-r--r-- | example/sample2-1.fq | 4000 | ||||
-rw-r--r-- | example/sample2-2.fq | 4000 |
7 files changed, 0 insertions, 97363 deletions
diff --git a/example/call.nix b/example/call.nix deleted file mode 100644 index c9be673..0000000 --- a/example/call.nix +++ /dev/null @@ -1,19 +0,0 @@ -# This is an example pipeline specification to do multi-sample variant calling -# with the Platypus variant caller. Each input is preprocessed by aligning -# against a reference genome (defaults to GRCH38), fixing mate information, and -# marking duplicates. Finally platypus is called over all samples. -{bionix ? import <bionix> {} -,nixpkgs ? import <nixpkgs> {} -,inputs -,ref ? null}: - -with bionix; - -let - preprocess = f: - samtools.markdup {} - (samtools.sort {} - (samtools.fixmate {} - (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;} f))); - - in platypus.call {} (map preprocess inputs) diff --git a/example/default.nix b/example/default.nix deleted file mode 100644 index bceaa96..0000000 --- a/example/default.nix +++ /dev/null @@ -1,42 +0,0 @@ -# This example uses the pipelines specified in the call.nix file on the -# synthetic data in this directory. -with import <bionix> {}; - -let - - # List of input samples - inputs = [ - # Sample 1 - { - input1 = fetchFastQ { - url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample1-1.fq"; - sha256 = "1m3vc248mbr4v56459q4xsklznssgqb35lwhwk1i9qvxqm7c72nq"; - }; - - input2 = fetchFastQ { - url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample1-2.fq"; - sha256 = "13fqvdb5r2sidi2i0s3ifg8gyxp8kibpxc3cbiw07d5zcn3g479x"; - }; - } - - # Sample 2 - { - input1 = fetchFastQ { - url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample2-1.fq"; - sha256 = "0c6ik4smsw2kb8xbbci80d00c24klk6mqd2a71y4v9hmpnc42fmr"; - }; - - input2 = fetchFastQ { - url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample2-2.fq"; - sha256 = "0zvrkm2m69lwfi89hzxsbnkp4i6cszh7c624l1qwmd4s6gh7vfcx"; - }; - } - ]; - - # The reference for the synthetic data - ref = fetchFastA { - url = "https://github.com/PapenfussLab/bionix/raw/master/example/ref.fa"; - sha256 = "06gphhh40h3mvwvs2m51qc3rpih8mcs8frhd48l94d5bzwfhb2hc"; - }; - -in import ./call.nix {inherit inputs ref;} diff --git a/example/ref.fa b/example/ref.fa deleted file mode 100644 index fdc51e6..0000000 --- a/example/ref.fa +++ /dev/null @@ -1,81302 +0,0 @@ ->SL1344 genome sequence -agagattacgtctggttgcaagagatcatgacagggggaattggttgaaaataaatatat -cgccagcagcacatgaacaagtttcggaatgtgatcaatttaaaaatttattgacttagg -cgggcagatactttaaccaatataggaatacaagacagacaaataaaaatgacagagtac -acaacatccatgaaccgcatcagcaccaccaccattaccaccatcaccattaccacaggt -aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgaacagtgcgg -gcttttttttcgaccagagatcacgaggtaacaaccatgcgagtgttgaagttcggcggt -acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc -aggcaagggcaggtagcgaccgtactttccgcccccgcgaaaattaccaaccatctggtg -gcaatgattgaaaaaactatcggcggccaggatgctttgccgaatatcagcgatgcagaa -cgtattttttctgacctgctcgcaggacttgccagcgcgcagccgggattcccgcttgca -cggttgaaaatggttgtcgaacaagaattcgctcagatcaaacatgttctgcatggtatc -agcctgctgggtcagtgcccggatagcatcaacgccgcgctgatttgccgtggcgaaaaa -atgtcgatcgcgattatggcgggacttctggaggcgcgtgggcatcgcgtcacggtgatc -gatccggtagaaaaattgctggcggtgggccattaccttgaatctaccgtcgatatcgcg -gaatcgactcgccgtatcgccgccagccagatcccggccgatcacatgatcctgatggcg -ggctttaccgccggtaatgaaaagggtgaactggtggtgctgggccgtaatggttccgac -tattccgccgccgtgctggccgcctgtttacgcgctgactgctgtgaaatctggactgac -gtcgatggcgtgtatacctgtgacccgcgccaggtgccggacgccaggctgctgaaatcg -atgtcctaccaggaagcgatggaactctcttacttcggcgccaaagtccttcaccctcgc -accattacgcccatcgcccagttccagatcccctgtctgattaaaaataccggtaatccg -caggcgccaggaacgctgatcggcgcgtccagcgacgatgataacctgccggttaaaggg -atctctaaccttaacaacatggcgatgtttagcgtctccggcccgggaatgaaagggatg -attgggatggcggcgcgtgttttcgccgccatgtctcgcgccgggatctcggtggtgctc -attacccagtcctcctctgagtacagcatcagtttctgtgtgccgcagagtgactgcgcg -cgtgcccgccgtgcgatgcaggatgagttctatctggagctgaaagaggggctgctggag -ccgctggcggttacggagcggttggcgattatctctgttgtcggcgacggtatgcgcacg -ctacgcggcatttcagcgaaattcttcgccgcgctggcgcgggctaatatcaatatcgtg -gcgatcgctcagggatcttctgagcgttctatttctgtggtggtgaataacgacgatgcc -accaccggcgtgcgggtaacgcaccagatgctgttcaataccgatcaggtgattgaagtg -tttgtcattggcgtcggcggcgtcggcggcgcgctactggaacagcttaaacgtcagcaa -acctggctgaagaacaagcacatcgatctacgcgtgtgcggcgtggcgaactcaaaggcg -ttgctaaccaatgtgcatggcctgaatctggacaactggcaggcggaactggcgcaagcg 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