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