Mercurial > repos > dcouvin > resfinder4
view resfinder/scripts/wdl/resfinder.wdl @ 0:55051a9bc58d draft default tip
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author | dcouvin |
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date | Mon, 10 Jan 2022 20:06:07 +0000 |
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workflow Resistance { File inputSamplesFile Array[Array[File]] inputSamples = read_tsv(inputSamplesFile) String outputDir Float geneCov Float geneID Float pointCov Float pointID String python String kma String blastn String resfinder String resDB String pointDB scatter (sample in inputSamples) { call ResFinder { input: inputSample=sample, outputRoot=outputDir, geneCov=geneCov, geneID=geneID, pointCov=pointCov, pointID=pointID, python=python, kma=kma, blastn=blastn, resfinder=resfinder, resDB=resDB, pointDB=pointDB } } } task ResFinder { Array[String] inputSample Float geneCov Float geneID Float pointCov Float pointID String python String kma String blastn String resfinder String resDB String pointDB String inputPath1 = inputSample[0] String inputPath2 = inputSample[1] String species = inputSample[2] String inputType = inputSample[3] String outputRoot String filename = basename(inputPath1) String out_dir_name = "${outputRoot}/${filename}.rf_out" command { set +u module unload mgmapper metabat fastqc module unload ncbi-blast perl source /home/projects/cge/apps/env/rf4_env/bin/activate module load perl module load ncbi-blast/2.8.1+ mkdir ${out_dir_name} inputArgs="" pointArgs="" if [ "${species}" = "other" ] && [ "${inputType}" = "paired" ] then inputArgs+="-ifq ${inputPath1} ${inputPath2}" elif [ "${inputType}" = "paired" ] then inputArgs+="-ifq ${inputPath1} ${inputPath2}" pointArgs+="--point --db_path_point ${pointDB} --min_cov_point ${pointCov} --threshold_point ${pointID}" elif [ "${species}" = "other"] && [ "${inputType}" = "assembly" ] then inputArgs+="-ifa ${inputPath1}" elif [ "${inputType}" = "assembly" ] then inputArgs+="-ifa ${inputPath1}" pointArgs+="--point --db_path_point ${pointDB} --min_cov_point ${pointCov} --threshold_point ${pointID}" fi ${python} ${resfinder} \ $inputArgs \ --blastPath ${blastn} \ --kmaPath ${kma} \ --species "${species}" \ --db_path_res ${resDB} \ --acquired \ --acq_overlap 30 \ --min_cov ${geneCov} \ --threshold ${geneID} \ -o ${out_dir_name} \ $pointArgs } output { File rf_out = "${out_dir_name}/std_format_under_development.json" } runtime { walltime: "1:00:00" cpu: 2 memory: "4 GB" queue: "cge" } }