Adding helper files and updating readme

[arvados-tutorial.git] / RNA-Seq / cwl / helper / alignment.cwl

diff --git a/RNA-Seq/cwl/helper/alignment.cwl b/RNA-Seq/cwl/helper/alignment.cwl
index 6712aae6b83c7957840320eeaf3597fb3d717827..e2a434fe3f3852f3e1771d16f2d908b4ee059c55 100644 (file)
--- a/RNA-Seq/cwl/helper/alignment.cwl
+++ b/RNA-Seq/cwl/helper/alignment.cwl
@@ -12,7 +12,7 @@ requirements:
 
 steps:
   fastqc:
 
 steps:
   fastqc:

-    run: bio-cwl-tools/fastqc/fastqc_2.cwl
+    run: fastqc_2.cwl

     in:
       reads_file: fq
     out: [html_file]
     in:
       reads_file: fq
     out: [html_file]


@@ -21,7 +21,7 @@ steps:
     requirements:
       ResourceRequirement:
         ramMin: 9000
     requirements:
       ResourceRequirement:
         ramMin: 9000

-    run: bio-cwl-tools/STAR/STAR-Align.cwl
+    run: STAR-Align.cwl

     in:
       RunThreadN: {default: 4}
       GenomeDir: genome
     in:
       RunThreadN: {default: 4}
       GenomeDir: genome


@@ -29,12 +29,11 @@ steps:
       OutSAMtype: {default: BAM}
       SortedByCoordinate: {default: true}
       OutSAMunmapped: {default: Within}
       OutSAMtype: {default: BAM}
       SortedByCoordinate: {default: true}
       OutSAMunmapped: {default: Within}

-      ### 1. Expressions on step inputs

       OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
     out: [alignment]
 
   samtools:
       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]
     in:
       bam_sorted: STAR/alignment
     out: [bam_sorted_indexed]