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-rw-r--r--examples/call.nix16
-rw-r--r--examples/default.nix9
-rw-r--r--examples/ex-nextflow/nextflow-example1.nix8
-rw-r--r--examples/ex-tnpair/cluster.nix14
-rw-r--r--examples/ex-tnpair/default.nix3
-rw-r--r--examples/ex-tnpair/tnpair.nix33
-rw-r--r--examples/ex-wdl/wdl-scatter-gather.nix5
7 files changed, 51 insertions, 37 deletions
diff --git a/examples/call.nix b/examples/call.nix
index 8a38fdb..81a112e 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -2,9 +2,10 @@
# 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> {}
-,inputs
-,ref ? bionix.ref.grch38.seq }:
+{ bionix ? import <bionix> { }
+, inputs
+, ref ? bionix.ref.grch38.seq
+}:
with bionix;
with lib;
@@ -13,9 +14,10 @@ let
preprocess = flip pipe [
(bwa.align { inherit ref; })
(samtools.sort { nameSort = true; })
- (samtools.fixmate {})
- (samtools.sort {})
- (samtools.markdup {})
+ (samtools.fixmate { })
+ (samtools.sort { })
+ (samtools.markdup { })
];
-in platypus.call {} (map preprocess inputs)
+in
+platypus.call { } (map preprocess inputs)
diff --git a/examples/default.nix b/examples/default.nix
index 9aace38..ef57341 100644
--- a/examples/default.nix
+++ b/examples/default.nix
@@ -1,6 +1,6 @@
# This example uses the pipelines specified in the call.nix file on the
# synthetic data in this directory.
-{bionix ? import <bionix> {}}:
+{ bionix ? import <bionix> { } }:
with bionix;
@@ -15,7 +15,7 @@ let
sha256 = "0kh29i6fg14dn0fb1xj6pkpk6d83y7zg7aphkbvjrhm82braqkm8";
};
- input2 = fetchFastQ {
+ input2 = fetchFastQ {
url = "https://github.com/PapenfussLab/bionix/raw/master/examples/sample1-2.fq";
sha256 = "0czk85km6a91y0fn4b7f9q7ps19b5jf7jzwbly4sgznps7ir2kdk";
};
@@ -28,7 +28,7 @@ let
sha256 = "08gixavfklqvk1m2ic6v56z82vl00qnpsd9xb64z6zl03nz98mcy";
};
- input2 = fetchFastQ {
+ input2 = fetchFastQ {
url = "https://github.com/PapenfussLab/bionix/raw/master/examples/sample2-2.fq";
sha256 = "1xxwm2vq52axpdhm14rh5mg5nzzpxaqnvhzrqhajm27fqksgzjjw";
};
@@ -41,4 +41,5 @@ let
sha256 = "0sy9hq8n55knfkiblam50dzaiwhrx6pv8b8l1njdn6kfj4wflz2p";
};
-in import ./call.nix {inherit inputs ref bionix;}
+in
+import ./call.nix { inherit inputs ref bionix; }
diff --git a/examples/ex-nextflow/nextflow-example1.nix b/examples/ex-nextflow/nextflow-example1.nix
index 4f00431..687505c 100644
--- a/examples/ex-nextflow/nextflow-example1.nix
+++ b/examples/ex-nextflow/nextflow-example1.nix
@@ -1,7 +1,8 @@
# This is a translation of the Nextflow example found at
# https://www.nextflow.io/example1.html
-{ bionix ? import ./../.. {}
-, input ? ./sample.fa}:
+{ bionix ? import ./../.. { }
+, input ? ./sample.fa
+}:
with bionix;
with lib;
@@ -24,7 +25,8 @@ let
'';
};
-in pipe input [
+in
+pipe input [
splitSequences
(each reverse)
]
diff --git a/examples/ex-tnpair/cluster.nix b/examples/ex-tnpair/cluster.nix
index 8d54995..5d4e1de 100644
--- a/examples/ex-tnpair/cluster.nix
+++ b/examples/ex-tnpair/cluster.nix
@@ -4,11 +4,12 @@ let
bionix = import <bionix> {
overlays = [
(_: super:
- super."${if tmpDir == null then "slurm" else "qsub"}" {
- ppn = 24;
- mem = 7;
- walltime = "3:00:00";
- } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })
+ super."${if tmpDir == null then "slurm" else "qsub"}"
+ {
+ ppn = 24;
+ mem = 7;
+ walltime = "3:00:00";
+ } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })
(self: super:
with super; {
@@ -27,4 +28,5 @@ let
})
];
};
-in import ./. { inherit bionix; }
+in
+import ./. { inherit bionix; }
diff --git a/examples/ex-tnpair/default.nix b/examples/ex-tnpair/default.nix
index f9581f8..65a2265 100644
--- a/examples/ex-tnpair/default.nix
+++ b/examples/ex-tnpair/default.nix
@@ -45,6 +45,7 @@ let
fetch = s: mapAttrs (_: fetchFastQGZ) s.inputs;
-in import ./tnpair.nix {
+in
+import ./tnpair.nix {
inherit pair fetch bionix;
}
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 9e6befe..414a391 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -1,4 +1,4 @@
-{bionix ? import <bionix> {}, pair, fetch}:
+{ bionix ? import <bionix> { }, pair, fetch }:
with bionix;
with lib;
@@ -13,7 +13,7 @@ let
fetch
(align { preset = "sr"; ref = ref.grch38.seq; flags = "-R'@RG\\tID:${s.type}\\tSM:${s.type}'"; })
(sort { nameSort = true; })
- (fixmate {})
+ (fixmate { })
(sort { })
(markdup { })
];
@@ -28,21 +28,26 @@ let
bams = mapAttrs (_: preprocess) pair;
- variants = let
- somatic = strelka.callSomatic { } bams; in mapAttrs (_: flip pipe [
- (compression.uncompress { })
- (snpeff.annotate { db = ref.grch38.snpeff.db; })
- dropErrors
- (snpeff.dbnsfp { dbnsfp = ref.grch38.snpeff.dbnsfp; })
- ]) {
- "snvs.vcf" = somatic.snvs;
- "indels.vcf" = somatic.snvs;
- "germline.vcf" = strelka.call { } [bams.normal];
- };
+ variants =
+ let
+ somatic = strelka.callSomatic { } bams; in
+ mapAttrs
+ (_: flip pipe [
+ (compression.uncompress { })
+ (snpeff.annotate { inherit (ref.grch38.snpeff) db; })
+ dropErrors
+ (snpeff.dbnsfp { inherit (ref.grch38.snpeff) dbnsfp; })
+ ])
+ {
+ "snvs.vcf" = somatic.snvs;
+ "indels.vcf" = somatic.snvs;
+ "germline.vcf" = strelka.call { } [ bams.normal ];
+ };
cnvs = cnvkit.callCNV { } { normals = [ bams.normal ]; tumours = [ bams.tumour ]; };
-in linkOutputs {
+in
+linkOutputs {
inherit variants;
alignments = linkOutputs (mapAttrs' (n: nameValuePair (n + ".bam")) bams);
cnvkit = cnvs;
diff --git a/examples/ex-wdl/wdl-scatter-gather.nix b/examples/ex-wdl/wdl-scatter-gather.nix
index 61dc441..5245662 100644
--- a/examples/ex-wdl/wdl-scatter-gather.nix
+++ b/examples/ex-wdl/wdl-scatter-gather.nix
@@ -1,6 +1,6 @@
# The scatter-gather example from https://github.com/openwdl/wdl
# translated to bionix
-{ bionix ? import ./../.. {} }:
+{ bionix ? import ./../.. { } }:
with bionix;
with lib;
@@ -30,4 +30,5 @@ let
'';
};
-in gather (map analysis prepare)
+in
+gather (map analysis prepare)