diff --git a/test_assembly.wdl b/test_assembly.wdl deleted file mode 100644 index dd68547..0000000 --- a/test_assembly.wdl +++ /dev/null @@ -1,71 +0,0 @@ -import "jgi_assembly.wdl" as jgi - -workflow test_assembly { - String bbtools_container="microbiomedata/bbtools:38.90" - String spades_container="microbiomedata/spades:3.15.0" - String validate_container="mbabinski17/comparejson:0.1" - String rename_contig_prefix="scaffold" - Float uniquekmer=1000 - String? memory="60G" - String? threads="8" - String? outdir="/vol_b/nmdc_workflows/test_nmdc/metaAssembly/test_output" - String url="https://portal.nersc.gov/cfs/m3408/test_data/Ecoli_10x-int.fastq.gz" - String ref_json="https://raw.githubusercontent.com/microbiomedata/metaAssembly/master/test_output/small_test_stats.json" - - call prepare { - input: container=bbtools_container, - url=url, - ref_json=ref_json - } - call jgi.jgi_metaASM as asm { - input: input_file=[prepare.fastq], - bbtools_container=bbtools_container, - spades_container=spades_container, - memory=memory, - threads=threads, - uniquekmer=uniquekmer, - rename_contig_prefix=rename_contig_prefix, - outdir=outdir - } - call validate { - input: container=validate_container, - refjson=prepare.refjson, - user_json=asm.final_asmstat - } -} -task prepare { - String container - String ref_json - String url - command{ - wget -O "input.fastq.gz" ${url} - wget -O "ref_json.json" ${ref_json} - } - output{ - File fastq = "input.fastq.gz" - File refjson = "ref_json.json" - } - runtime { - memory: "1 GiB" - cpu: 2 - maxRetries: 1 - docker: container - } -} -task validate { - String container - File refjson - File user_json - command { - compare_json.py -i ${refjson} -f ${user_json} - } - output { - Array[String] result = read_lines(stdout()) - } - runtime { - memory: "1 GiB" - cpu: 1 - maxRetries: 1 - docker: container - } -}