19952 Organizing helper files

[lightning.git] / cwl / lightning / lightning-slice-numpy-anno2vcf-wf.cwl

diff --git a/cwl/lightning/lightning-slice-numpy-anno2vcf-wf.cwl b/cwl/lightning/lightning-slice-numpy-anno2vcf-wf.cwl
index 874bc41aed6f9ef12e32cd2f214aecd45d42d31b..e60eb7a3fc6ea09f9f3cafb8ea682209fd2c553a 100644 (file)
--- a/cwl/lightning/lightning-slice-numpy-anno2vcf-wf.cwl
+++ b/cwl/lightning/lightning-slice-numpy-anno2vcf-wf.cwl
@@ -43,14 +43,14 @@ outputs:
 
 steps:
   lightning-tiling-stats:
-    run: lightning-tiling-stats.cwl
+    run: helpers/lightning-tiling-stats.cwl
     when: $(inputs.regions == null)
     in:
       libdir: libdir
     out: [bed]
 
   lightning-slice-numpy:
-    run: lightning-slice-numpy.cwl
+    run: helpers/lightning-slice-numpy.cwl
     in:
       matchgenome: matchgenome
       libdir: libdir
@@ -61,7 +61,7 @@ steps:
     out: [outdir, npys, samplescsv, chunktagoffsetcsv]
 
   lightning-slice-numpy-onehot:
-    run: lightning-slice-numpy-onehot.cwl
+    run: helpers/lightning-slice-numpy-onehot.cwl
     in:
       matchgenome: matchgenome
       libdir: libdir
@@ -73,7 +73,7 @@ steps:
     out: [outdir, npys, samplescsv]
 
   lightning-anno2vcf-onehot:
-    run: lightning-anno2vcf.cwl
+    run: helpers/lightning-anno2vcf.cwl
     in:
       annodir: lightning-slice-numpy-onehot/outdir
     out: [vcfdir]
@@ -91,7 +91,7 @@ steps:
     out: [annotatedvcf, summary]
 
   stage-output:
-    run: stage-output.cwl
+    run: helpers/stage-output.cwl
     in:
       libname: libname
       npyfiles:
@@ -106,7 +106,7 @@ steps:
     out: [stagednpydir, stagedonehotnpydir, stagedannotationdir]
 
   genreadme:
-    run: genreadme.cwl
+    run: helpers/genreadme.cwl
     in:
       samplescsv: lightning-slice-numpy/samplescsv
       readmeinfo: readmeinfo