Modernize readmapping example

examples/readmapping/workflow.py

@@ -1,6 +1,6 @@
 """This is an example workflow for read-mapping using bwa and samtools."""
 
-from gwf import Workflow
+from gwf import Workflow, AnonymousTarget
 
 gwf = Workflow()
 
@@ -18,7 +18,8 @@ def unzip(inputfile, outputfile):
     gzcat {} > {}
     '''.format(inputfile, outputfile)
 
-    return inputs, outputs, options, spec
+    return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
+
 
 def bwa_index(ref_genome):
     """Template for indexing a genome with `bwa index`."""
@@ -38,7 +39,8 @@ def bwa_index(ref_genome):
     bwa index -p {ref_genome} -a bwtsw {ref_genome}.fa
     """.format(ref_genome=ref_genome)
 
-    return inputs, outputs, options, spec
+    return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
+
 
 def bwa_map(ref_genome, r1, r2, bamfile):
     """Template for mapping reads to a reference genome with `bwa` and `samtools`."""
@@ -59,18 +61,30 @@ def bwa_map(ref_genome, r1, r2, bamfile):
     samtools rmdup -s - {bamfile}
     '''.format(ref_genome=ref_genome, r1=r1, r2=r2, bamfile=bamfile)
 
-    return inputs, outputs, options, spec
-
-
-gwf.target_from_template('UnzipGenome',
-                         unzip(inputfile='ponAbe2.fa.gz',
-                               outputfile='ponAbe2.fa'))
-
-gwf.target_from_template('IndexGenome',
-                         bwa_index(ref_genome='ponAbe2'))
-
-gwf.target_from_template('MapReads',
-                         bwa_map(ref_genome='ponAbe2',
-                                 r1='Masala_R1.fastq.gz',
-                                 r2='Masala_R2.fastq.gz',
-                                 bamfile='Masala.bam'))
+    return AnonymousTarget(inputs=inputs, outputs=outputs, options=options, spec=spec)
+
+
+gwf.target_from_template(
+    name='UnzipGenome',
+    template=unzip(
+        inputfile='ponAbe2.fa.gz',
+        outputfile='ponAbe2.fa'
+    )
+)
+
+gwf.target_from_template(
+    name='IndexGenome',
+    template=bwa_index(
+        ref_genome='ponAbe2'
+    )
+)
+
+gwf.target_from_template(
+    name='MapReads',
+    template=bwa_map(
+        ref_genome='ponAbe2',
+        r1='Masala_R1.fastq.gz',
+        r2='Masala_R2.fastq.gz',
+        bamfile='Masala.bam'
+    )
+)