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[rnaseq-cwl-training.git] / answers / ep6 / alignment.cwl

diff --git a/answers/ep6/alignment.cwl b/answers/ep6/alignment.cwl
deleted file mode 100644 (file)
index 8a54fe4..0000000
--- a/answers/ep6/alignment.cwl
+++ /dev/null
@@ -1,47 +0,0 @@
-cwlVersion: v1.2
-class: Workflow
-label: RNAseq CWL practice workflow
-
-inputs:
-  fq: File
-  genome: Directory
-  gtf: File
-
-requirements:
-  StepInputExpressionRequirement: {}
-
-steps:
-  fastqc:
-    run: bio-cwl-tools/fastqc/fastqc_2.cwl
-    in:
-      reads_file: fq
-    out: [html_file]
-
-  STAR:
-    requirements:
-      ResourceRequirement:
-        ramMin: 6000
-    run: bio-cwl-tools/STAR/STAR-Align.cwl
-    in:
-      RunThreadN: {default: 4}
-      GenomeDir: genome
-      ForwardReads: fq
-      OutSAMtype: {default: BAM}
-      OutSAMunmapped: {default: Within}
-      ### 1. Expressions on step inputs
-      OutFileNamePrefix: {valueFrom: "$(inputs.ForwardReads.nameroot)."}
-    out: [alignment]
-
-  samtools:
-    run: bio-cwl-tools/samtools/samtools_index.cwl
-    in:
-      bam_sorted: STAR/alignment
-    out: [bam_sorted_indexed]
-
-outputs:
-  qc_html:
-    type: File
-    outputSource: fastqc/html_file
-  bam_sorted_indexed:
-    type: File
-    outputSource: samtools/bam_sorted_indexed