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1 #!/usr/bin/env nextflow
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2
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3 python3 = "python3"
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4 resfinder = "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py"
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5
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6 params.input = './*.fa'
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7 // params.indir = './'
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8 // params.ext = '.fa'
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9 params.outdir = '.'
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10 params.species = 'other'
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11
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12 println("Search pattern: $params.input")
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13
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14 infile_ch = Channel
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15 .fromPath("$params.input", followLinks: true)
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16 .map{ file -> tuple(file.baseName, file) }
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17
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18 process resfinder{
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19
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20 cpus 1
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21 time '30m'
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22 memory '1 GB'
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23 clusterOptions '-V -W group_list=cge -A cge'
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24 executor "PBS"
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25
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26 input:
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27 set sampleID, file(datasetFile) from infile_ch
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28
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29 output:
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30 stdout result
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31
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32 """
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33 set +u
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34 module unload mgmapper metabat fastqc
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35 module unload ncbi-blast perl
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36 source /home/projects/cge/apps/env/rf4_env/bin/activate
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37 module load perl
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38 module load ncbi-blast/2.8.1+
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39 if [ $params.species = 'other' ]
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40 then
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41 $python3 $resfinder -acq -ifa $datasetFile -o '$params.outdir/$sampleID' -s '$params.species'
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42 else
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43 $python3 $resfinder -acq -ifa $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' --point
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44 fi
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45 """
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46 }
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47
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48 /*
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49 result.subscribe {
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50 println it
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51 }
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52 */
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