Arc cwl

arc-job.yml

+################################################################################
+### runs/kallisto
+################################################################################
+
+## Genome file to build kallisto Index
+kallisto_IndexInput:
+  - class: File
+    path: ./studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa
+    format: edam:format_1929 # FASTA
+
+## Fastq files to be mapped
+# The `readsOfOneSample` looks more complicated than needed
+# It's an array of records (each with one or mupltiple files and a sample name) to generically allow multiple fastq files per sample
+
+kallisto_sampleRecord:
+  - readsOfOneSample:
+    - class: File
+      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
+      format: edam:format_1930
+    sampleName: 'DB_163'
+  - readsOfOneSample:
+    - class: File
+      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
+      format: edam:format_1930
+    sampleName: 'DB_103'
+  - readsOfOneSample:
+    - class: File
+      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
+      format: edam:format_1930
+    sampleName: 'DB_165'
+
+### Kallisto quant Parameters
+kallisto_isSingle: true
+kallisto_FragmentLength: 200
+kallisto_StandardDeviation: 20
+kallisto_BootstrapSamples: 30
+kallisto_resultsFolder: kallisto_results
+
+$namespaces:
+  edam: https://edamontology.org/
+
+################################################################################
+### runs/isaSampleToRawDataSeq
+################################################################################
+
+isaSampleToRawDataSeq_arcPath: 
+  class: Directory
+  path: ./
+isaSampleToRawDataSeq_assayName: "RNASeq"
+isaSampleToRawDataSeq_outName: rnaseq-samples
+isaSampleToRawDataSeq_startingNodeNum: 0
+
+################################################################################
+### runs/sleuth
+################################################################################
+
+sleuth_inMetadataSample: "Input [Source Name]"
+sleuth_inMetadataFactorList:
+  - "Factor [Photosynthesis mode]"
+sleuth_inMetadataDataCol: "Output [Data]"
+sleuth_outFolder: results