Arc cwl

arc-job.yml

@@ -5,7 +5,7 @@
 ## Genome file to build kallisto Index
 kallisto_IndexInput:
   - class: File
-    path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+    path: ./studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
     format: edam:format_1929 # FASTA
 
 ## Fastq files to be mapped
@@ -15,32 +15,32 @@ kallisto_IndexInput:
 kallisto_sampleRecord:
   - readsOfOneSample:
     - class: File
-      path: ../../assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
+      path: ./assays/RNASeq/dataset/DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz
       format: edam:format_1930
     sampleName: 'DB_097'
   - readsOfOneSample:  
     - class: File
-      path: ../../assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
+      path: ./assays/RNASeq/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz
       format: edam:format_1930
     sampleName: 'DB_163'
   - readsOfOneSample:
     - class: File
-      path: ../../assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
+      path: ./assays/RNASeq/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz
       format: edam:format_1930
     sampleName: 'DB_099'
   - readsOfOneSample:
     - class: File
-      path: ../../assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
+      path: ./assays/RNASeq/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz
       format: edam:format_1930
     sampleName: 'DB_103'
   - readsOfOneSample:
     - class: File
-      path: ../../assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
+      path: ./assays/RNASeq/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz
       format: edam:format_1930
     sampleName: 'DB_161'
   - readsOfOneSample:
     - class: File
-      path: ../../assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
+      path: ./assays/RNASeq/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz
       format: edam:format_1930
     sampleName: 'DB_165'
 
@@ -60,7 +60,7 @@ $namespaces:
 
 isaSampleToRawDataSeq_arcPath: 
   class: Directory
-  path: ../../
+  path: ./
 isaSampleToRawDataSeq_assayName: "RNASeq"
 isaSampleToRawDataSeq_outName: rnaseq-samples
 isaSampleToRawDataSeq_startingNodeNum: 0