{"id": "file:///Users/leipzig/Documents/dev/truwl/capanno/cwl-tools/spades/3.15.0/spades_spades/spades-spades.cwl", "doc": "example workflow for js wrapper generation\nsee https://github.com/rrwick/Unicycler\noutputs : all genretated files\n", "class": "CommandLineTool", "hints": [{"class": "DockerRequirement", "dockerPull": "truwl/spades:3.15.0_0.1.0"}, {"class": "SoftwareRequirement", "packages": {"spades": {"specs": ["http://identifiers.org/biotools/spades"], "version": ["3.15.0"]}}}], "inputs": [], "outputs": [{"id": "all_log", "doc": "spades output log and warnings", "type": [{"name": "_:2a90b09e-5780-4fb3-b0c3-47c57d606621", "type": "array", "items": "File"}], "outputBinding": {"glob": "*.log"}}, {"id": "assembly_graph", "doc": "assembly graph", "type": "File", "outputBinding": {"glob": "assembly_graph.fastg"}}, {"id": "assembly_graph_with_scaffolds", "doc": "assembly graph with scaffolds", "type": "File", "outputBinding": {"glob": "assembly_graph_with_scaffolds.gfa"}}, {"id": "out_contig_stats", "doc": "contig stats, default column_names: name,length,coverage", "type": "File", "outputBinding": {"glob": "out_contig_stats.*"}}, {"id": "out_contigs", "doc": "contigs (fasta sequence)", "type": "File", "outputBinding": {"glob": "contigs.fasta"}}, {"id": "out_scaffold_stats", "doc": "scaffold stats, default column_names: name,length,coverage", "type": "File", "outputBinding": {"glob": "out_scaffold_stats.*"}}, {"id": "out_scaffolds", "doc": "scaffolds (fasta sequence)", "type": "File", "outputBinding": {"glob": "scaffolds.fasta"}}], "arguments": ["spades_wrapper.sh"], "cwlVersion": "v1.0", "baseCommand": ["bash"], "requirements": [{"class": "InitialWorkDirRequirement", "listing": [{"entry": "#######input file here\n#!/usr/bin/env python\nimport sys,re\nsearch_str = r'^>(NODE|\\S+)_(\\d+)(?:_|\\s)length_(\\d+)_cov_(\\d+\\.*\\d*).*\\$'\nreplace_str = r'\\1_\\2\\t\\3\\t\\4'\ncmd = re.compile(search_str)\nsys.stdout.write('#name\\tlength\\tcoverage\\n')\nfor i,line in enumerate(sys.stdin):\n if cmd.match(line):\n sys.stdout.write(cmd.sub(replace_str,line))\n", "entryname": "write_tsv.py"}, {"entry": "####################spades launcher\n#!/bin/bash\n## An example command looks like:\n## spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output \nread -d '' MEMORY_GB << EOF\n${ \n //compute memory limits\n var mem=\"250\"\n if(runtime.ram){\n var bt=runtime.ram * 1048576 //mebibytes to bytes \n bt=bt*0.000000001 //bytes to Gigabytes \n mem=parseInt(bt)\n }\n return \"-\"+mem\n}\nEOF\n#echo \"MEMORY_GB limit: \\$MEMORY_GB\"\nread -d '' CORES << EOF\n${ \n //compute core / slot\n var cores=\"16\" \n if(runtime.cores){\n cores=runtime.cores\n }\n return cores\n}\nEOF\n#echo \"CORES : \\$CORES\"\nread -d '' SPADES_OPT << EOF\n${ \n var opt=\"\"\n if (inputs.sc==true){\n opt+=\" --sc \"\n }\n if (inputs.onlyassembler==true){\n opt+=\" --only-assembler \"\n }\n if (inputs.careful==true){\n opt+=\" --careful \"\n }\n return opt \n}\nEOF\n\n\nread -d '' CMD_BASE << EOF\nspades.py -o . --disable-gzip-output \n \\$SPADES_OPT \n -t \\$CORES -m \\$MEMORY_GB\n${ \n var opt=\"\"\n if (inputs.auto_kmer_choice==false){\n opt+=\" -k \"+inputs.kmers \n }\n return opt \n}\n${\n var opt=\"\"\n if (inputs.cov_state==null || inputs.cov_state == \"auto\"){\n opt+=\" --cov-cutoff 'auto' \"\n }\n else if (inputs.cov_state == \"value\"){\n opt+=\" --cov-cutoff '\"+inputs.cov_cutoff+\"' \"\n }\n if (inputs.iontorrent==true ){\n opt+=\" --iontorrent \"\n } \n return opt \n}\nEOF\n##########################################\n##Sequence files from libraries\nread -d '' CMD_READ1 << EOF\n${\nvar opt=\"\"\nvar lib_prefix = {}\nvar lib_meta=inputs.libraries_metadata \nif (lib_meta!=null){\n for(var j=0; jDEBUG\n\n##########################################\n##Sequence files from libraries\nread -d '' ZZDEBUG << EOF\n${\n//var opt=\"inputs.libraries_metadata.length:\"+inputs.libraries_metadata.length+\" \" \n//var str = JSON.stringify(inputs.libraries_metadata)\nvar opt=\"\"\nvar lib_prefix = {}\nvar lib_meta=inputs.libraries_metadata \nif (lib_meta!=null){\n opt+=\" not null \"\n for(var j=0; j out_contig_stats.tab\n && python write_tsv.py < scaffolds.fasta > out_scaffold_stats.tab\nEOF\n########################################## \n# echo \"CMD_BASE : \\$CMD_BASE\" > zz.txt \\\\\n# && echo \"CMD_READ1 : \\$CMD_READ1\" >> zz.txt \\\\\n# && echo \"CMD_READ2 : \\$CMD_READ2\" >> zz.txt \\\\\n# && echo \"CMD_POST : \\$CMD_POST\" >> zz.txt\nCOMMAND=\"\\$CMD_BASE \\$CMD_READ1 \\$CMD_READ2 \\$CMD_POST\"\nCOMMAND=\\$(echo $COMMAND|tr -d '\\\\n')\necho \"\\$COMMAND\" > run_spades.sh\nbash ./run_spades.sh\n", "entryname": "spades_wrapper.sh"}]}, {"class": "InlineJavascriptRequirement"}]}

spades spades

Version:3.15.0

Identifier: TL_b5fc93_b5.59

Tool

Version:
3.15.0