7 files changed, 65 insertions, 74 deletions
diff --git a/abcbs_2018.md b/abcbs_2018.md
deleted file mode 100644
index a8adc45..0000000
--- a/abcbs_2018.md
+++ /dev/null
@@ -1,44 +0,0 @@
-**Nix for reproducible research**
-
-Justin Bedő, Leon Di Stefano, and Tony Papenfuss
-
-> A challenge for bioinformaticians is to make our computations reproducible — that is, easy to rerun, combine, share, and guaranteed to generate the same results.
-> We show how Nix, a next generation cross-platform software deployment system, cleanly overcomes problems usually tackled with a combination of package managers (e.g., conda), containers (e.g., Docker, Singularity), and workflow engines (e.g., Toil, Ruffus).
-> 
-> On its own Nix can be used as a package manager; it can also easily create isolated development environments and export portable containers to share with others.
-> We have created a number of transparent and lightweight extensions that enable Nix to succinctly specify bioinformatics analysis environments and pipelines locally, in HPC environments, or in the cloud.
-> 
-> Nix uses hash-based naming to ensure that what it builds is uniquely specified, isolation and completeness to ensure that its build processes are deterministic, and a simple programming language to ensure that the whole system is easy to manage.
-> It has an extensive package collection, which includes all of CRAN and Bioconductor, and the conda package manager allowing access to Bioconda recipes.
-> Nix is well supported and general-purpose software that has been in development for over 10 years.
-> 
-> We will demonstrate how Nix with our extensions can be used to succinctly specify a typical bioinformatics pipeline and contrast this against other dedicated bioinformatics pipeline languages.
-> We then show how it can be executed in whole or in part on an HPC queuing system
-> Finally, we show that the pipeline can also be executed using cloud resources.
-
-### Stuff to match in competitors
-
--   **A few standard pipelines**
--   Dealing with big files
--   Slightly complicated analyses
--   local, HPC, and cloud execution
--   Resumable, parallel
--   Bioconda import
-
-### Points of difference
-
--   **Full-stack reproduciblity with one tool**
--   **A language rather than a configuration format (cf. CWL/Javascript)**
--   Not bioinformatics-specific
--   Mature (~10y)
--   Containers obsolete (but easy to generate)
--   Higher level of reproducibility overall (hashing of inputs, outputs, derivations)
--   Safety
-    -   Declarative language
-    -   Type/tag system (to do)
-
-### Weaknesses
-
--   Small bioinformatics collection
--   No build execution stats
--   Subtleties around filesystems and the Nix store
diff --git a/conda.nix b/conda.nix
deleted file mode 100644
index bbcb7cf..0000000
--- a/conda.nix
+++ /dev/null
@@ -1,28 +0,0 @@
-{ stdenv, lib, writeScript, conda }:
-
-{
-  buildCondaEnv = { depends ? [], run }: stdenv.mkDerivation {
-    name = "conda-env";
-    propagatedBuildInputs = [ conda ] ++ depends;
-    buildCommand = ''
-      mkdir $out
-      HOME=$out
-      conda-shell-4.3.31 << EOF
-      conda-install
-      ${run}
-      EOF
-    '';
-  };
-
-  inCondaEnv = env: run: stdenv.mkDerivation {
-    name = "with-conda-env";
-    buildCommand = ''
-      #!${stdenv.shell}
-      export HOME=${env}
-      ${conda}/bin/conda-shell-4.3.31 << EOF
-      ${run}
-      EOF
-    '';
-  };
-}
-
diff --git a/examples/ex-nextflow/nextflow-example1.nix b/examples/ex-nextflow/nextflow-example1.nix
new file mode 100644
index 0000000..b31984a
--- /dev/null
+++ b/examples/ex-nextflow/nextflow-example1.nix
@@ -0,0 +1,30 @@
+# This is a translation of the Nextflow example found at
+# https://www.nextflow.io/example1.html
+{ bionix ? import <bionix> {}
+, input ? ./sample.fa}:
+
+with bionix;
+with lib;
+
+let
+  splitSequences = fa: stage {
+    name = "splitSequences";
+    buildInputs = [ pkgs.gawk ];
+    buildCommand = ''
+      awk '/^>/{f="seq_"++d} {print > f}' ${fa}
+      mkdir $out
+      cp seq* $out
+    '';
+  };
+
+  reverse = fa: stage {
+    name = "reverse";
+    buildCommand = ''
+      ${pkgs.utillinux}/bin/rev ${fa} > $out
+    '';
+  };
+
+in pipe [
+  splitSequences
+  (each reverse)
+] input
diff --git a/examples/tnpair b/examples/ex-tnpair/tnpair
index 5b84d5c..5b84d5c 100755
--- a/examples/tnpair
+++ b/examples/ex-tnpair/tnpair
diff --git a/examples/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 2939db4..2939db4 100644
--- a/examples/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
diff --git a/examples/ex-wdl/wdl-scatter-gather.nix b/examples/ex-wdl/wdl-scatter-gather.nix
new file mode 100644
index 0000000..387d382
--- /dev/null
+++ b/examples/ex-wdl/wdl-scatter-gather.nix
@@ -0,0 +1,33 @@
+# The scatter-gather example from https://github.com/openwdl/wdl
+# translated to bionix
+{ bionix ? import <bionix> {} }:
+
+with bionix;
+with lib;
+
+let
+
+  prepare = splitString "\n" (removeSuffix "\n" (readFile (stage {
+    name = "prepare";
+    buildInputs = [ pkgs.python3 ];
+    buildCommand = ''
+      python -c "print('one\ntwo\nthree\nfour', end=''')" > $out
+    '';
+  })));
+
+  analysis = str: removeSuffix "\n" (readFile (stage {
+    name = "analysis";
+    buildInputs = [ pkgs.python ];
+    buildCommand = ''
+      python -c "print('_${str}_')" > $out
+    '';
+  }));
+
+  gather = strs: stage {
+    name = "gather";
+    buildCommand = ''
+      echo ${concatStringsSep " " strs} > $out
+    '';
+  };
+
+in gather (map analysis prepare)
diff --git a/test-tnpair.nix b/test-tnpair.nix
index cd8620a..1d281fa 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -49,8 +49,8 @@ let
     (ln (strelka.snvs tnpairResult.variants) "strelka.snvs.vcf")
     (ln (strelka.variants tnpairResult.glvariants) "strelka.gl.vcf")
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
-    (ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam")
-    (ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam")
+    #(ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam")
+    #(ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam")
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
     (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
     (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3")