Mercurial > repos > dcouvin > resfinder4
comparison resfinder/scripts/resfinder_asm.nf @ 0:55051a9bc58d draft default tip
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| author | dcouvin |
|---|---|
| date | Mon, 10 Jan 2022 20:06:07 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:55051a9bc58d |
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| 1 #!/usr/bin/env nextflow | |
| 2 | |
| 3 python3 = "python3" | |
| 4 resfinder = "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py" | |
| 5 | |
| 6 params.input = './*.fa' | |
| 7 // params.indir = './' | |
| 8 // params.ext = '.fa' | |
| 9 params.outdir = '.' | |
| 10 params.species = 'other' | |
| 11 | |
| 12 println("Search pattern: $params.input") | |
| 13 | |
| 14 infile_ch = Channel | |
| 15 .fromPath("$params.input", followLinks: true) | |
| 16 .map{ file -> tuple(file.baseName, file) } | |
| 17 | |
| 18 process resfinder{ | |
| 19 | |
| 20 cpus 1 | |
| 21 time '30m' | |
| 22 memory '1 GB' | |
| 23 clusterOptions '-V -W group_list=cge -A cge' | |
| 24 executor "PBS" | |
| 25 | |
| 26 input: | |
| 27 set sampleID, file(datasetFile) from infile_ch | |
| 28 | |
| 29 output: | |
| 30 stdout result | |
| 31 | |
| 32 """ | |
| 33 set +u | |
| 34 module unload mgmapper metabat fastqc | |
| 35 module unload ncbi-blast perl | |
| 36 source /home/projects/cge/apps/env/rf4_env/bin/activate | |
| 37 module load perl | |
| 38 module load ncbi-blast/2.8.1+ | |
| 39 if [ $params.species = 'other' ] | |
| 40 then | |
| 41 $python3 $resfinder -acq -ifa $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' | |
| 42 else | |
| 43 $python3 $resfinder -acq -ifa $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' --point | |
| 44 fi | |
| 45 """ | |
| 46 } | |
| 47 | |
| 48 /* | |
| 49 result.subscribe { | |
| 50 println it | |
| 51 } | |
| 52 */ |