X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/5b4f2a85bedfad9e72e406e3e1990afc913c9da2..bec60d8f8671fedf159d9be0c02196ebaf602d53:/RNA-Seq/cwl/helper/alignment.cwl

diff --git a/RNA-Seq/cwl/helper/alignment.cwl b/RNA-Seq/cwl/helper/alignment.cwl
index 6712aae..e2a434f 100644
--- a/RNA-Seq/cwl/helper/alignment.cwl
+++ b/RNA-Seq/cwl/helper/alignment.cwl
@@ -12,7 +12,7 @@ requirements:
 
 steps:
   fastqc:
-    run: bio-cwl-tools/fastqc/fastqc_2.cwl
+    run: fastqc_2.cwl
     in:
       reads_file: fq
     out: [html_file]
@@ -21,7 +21,7 @@ steps:
     requirements:
       ResourceRequirement:
         ramMin: 9000
-    run: bio-cwl-tools/STAR/STAR-Align.cwl
+    run: STAR-Align.cwl
     in:
       RunThreadN: {default: 4}
       GenomeDir: genome
@@ -29,12 +29,11 @@ steps:
       OutSAMtype: {default: BAM}
       SortedByCoordinate: {default: true}
       OutSAMunmapped: {default: Within}
-      ### 1. Expressions on step inputs
       OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
     out: [alignment]
 
   samtools:
-    run: bio-cwl-tools/samtools/samtools_index.cwl
+    run: samtools_index.cwl
     in:
       bam_sorted: STAR/alignment
     out: [bam_sorted_indexed]