cwlVersion: v1.1
class: CommandLineTool
-label: Realigning fastqs and converting output to bam
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Align FASTQs with BWA
requirements:
DockerRequirement:
- dockerPull: curii/bwa-samtools-picard
+ dockerPull: curii/bwa-samtools
ShellCommandRequirement: {}
- ResourceRequirement:
- ramMin: 26000
- coresMin: 16
hints:
arv:RuntimeConstraints:
+ keep_cache: 1024
outputDirType: keep_output_dir
+ ResourceRequirement:
+ ramMin: 50000
+ coresMin: 16
+ SoftwareRequirement:
+ packages:
+ BWA:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_010910" ]
+ version: [ "0.7.17" ]
+ Samtools:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ]
+ version: [ "1.10" ]
inputs:
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- .sa
- .fai
- ^.dict
- fastq1: File
- fastq2: File
- sample: string
+ fastq1:
+ type: File
+ format: edam:format_1930 # FASTQ
+ label: One of set of pair-end FASTQs (R1)
+ fastq2:
+ type: File
+ format: edam:format_1930 # FASTQ
+ label: One of set of pair-end FASTQs (R2)
+ sample:
+ type: string
+ label: Sample Name
stdout: $(inputs.sample).bam
outputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Alignments in BAM format
outputBinding:
glob: "*bam"
- $(runtime.cores)
- $(inputs.reference)
- -R
- - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
+ - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
- -c
- '250'
- $(inputs.fastq1)
- -S
- shellQuote: false
valueFrom: '-'
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl