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comparison resfinder/scripts/wdl/resfinder.wdl @ 0:a16d245332d6 draft default tip

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author dcouvin
date Wed, 08 Dec 2021 01:46:07 +0000
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-1:000000000000 0:a16d245332d6
1 workflow Resistance {
2 File inputSamplesFile
3 Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
4
5 String outputDir
6 Float geneCov
7 Float geneID
8 Float pointCov
9 Float pointID
10 String python
11 String kma
12 String blastn
13 String resfinder
14 String resDB
15 String pointDB
16
17 scatter (sample in inputSamples) {
18 call ResFinder {
19 input: inputSample=sample,
20 outputRoot=outputDir,
21 geneCov=geneCov,
22 geneID=geneID,
23 pointCov=pointCov,
24 pointID=pointID,
25 python=python,
26 kma=kma,
27 blastn=blastn,
28 resfinder=resfinder,
29 resDB=resDB,
30 pointDB=pointDB
31 }
32 }
33 }
34
35 task ResFinder {
36
37 Array[String] inputSample
38 Float geneCov
39 Float geneID
40 Float pointCov
41 Float pointID
42 String python
43 String kma
44 String blastn
45 String resfinder
46 String resDB
47 String pointDB
48
49 String inputPath1 = inputSample[0]
50 String inputPath2 = inputSample[1]
51 String species = inputSample[2]
52 String inputType = inputSample[3]
53
54 String outputRoot
55 String filename = basename(inputPath1)
56 String out_dir_name = "${outputRoot}/${filename}.rf_out"
57
58 command {
59
60 set +u
61 module unload mgmapper metabat fastqc
62 module unload ncbi-blast perl
63 source /home/projects/cge/apps/env/rf4_env/bin/activate
64 module load perl
65 module load ncbi-blast/2.8.1+
66
67 mkdir ${out_dir_name}
68
69 inputArgs=""
70 pointArgs=""
71
72 if [ "${species}" = "other" ] && [ "${inputType}" = "paired" ]
73 then
74 inputArgs+="-ifq ${inputPath1} ${inputPath2}"
75 elif [ "${inputType}" = "paired" ]
76 then
77 inputArgs+="-ifq ${inputPath1} ${inputPath2}"
78 pointArgs+="--point --db_path_point ${pointDB} --min_cov_point ${pointCov} --threshold_point ${pointID}"
79 elif [ "${species}" = "other"] && [ "${inputType}" = "assembly" ]
80 then
81 inputArgs+="-ifa ${inputPath1}"
82 elif [ "${inputType}" = "assembly" ]
83 then
84 inputArgs+="-ifa ${inputPath1}"
85 pointArgs+="--point --db_path_point ${pointDB} --min_cov_point ${pointCov} --threshold_point ${pointID}"
86 fi
87
88 ${python} ${resfinder} \
89 $inputArgs \
90 --blastPath ${blastn} \
91 --kmaPath ${kma} \
92 --species "${species}" \
93 --db_path_res ${resDB} \
94 --acquired \
95 --acq_overlap 30 \
96 --min_cov ${geneCov} \
97 --threshold ${geneID} \
98 -o ${out_dir_name} \
99 $pointArgs
100 }
101 output {
102 File rf_out = "${out_dir_name}/std_format_under_development.json"
103 }
104 runtime {
105 walltime: "1:00:00"
106 cpu: 2
107 memory: "4 GB"
108 queue: "cge"
109 }
110 }