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planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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1 #!/usr/bin/env nextflow
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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2 nextflow.enable.dsl=2
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3
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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4
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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5 /*
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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6 *Execution of:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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7 * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/diamond
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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8 * -asn-cache /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/sequence_cache
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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9 * -blastp-args '--sam-query-len --comp-based-stats 0 --evalue 0.0001 --very-sensitive --max-hsps 3'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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10 * -diamond-executable /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/third-party/diamond/diamond
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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11 * -lds2 /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/prot_gnomon_prepare.8202002/out/LDS2
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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12 * -ofmt seq-align-set
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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13 * -output-dir /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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14 * -output-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out/align.mft
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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15 * -output-prefix hits
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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16 * ## query is gnomon-made proteins 'gnl|GNOMON|23016146.p'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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17 * ## query-fmt is <String, `fasta', `seq-ids'>
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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18 * -query-fmt seq-ids
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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19 * -query-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/query_ids.mft
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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20 * ## subject is swiss-prot ids 'sp|A0A009IHW8.1|ABTIR_ACIB9'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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21 * -subject-fmt seq-ids
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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22 * -subject-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/subject_ids.mft
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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23 * -work-area /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/tmp
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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25 */
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d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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27 include {to_map; shellSplit } from '../../utilities'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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30 swiss_prot_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/reference_sets/swissprot.asnb.gz'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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31 process fetch_swiss_prot_asn {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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32 input:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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33 output:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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34 path "output/swissprot.asnb", emit: "swiss_prot_asn"
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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35 script:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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36 """
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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37 curl -O '$swiss_prot_url'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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38 gunzip swissprot.asnb.gz
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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39 mkdir -p output
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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40 mv swissprot.asnb output/swissprot.asnb
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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41 """
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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42 stub:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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43 """
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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44 mkdir -p output
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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45 touch output/swissprot.asnb
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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46 """
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47 }
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48
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49 process get_swiss_prot_ids {
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50 input:
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51 path swiss_prot_asn
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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52 output:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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53 path "output/swiss_prot_ids"
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54 script:
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55 """
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56 mkdir -p output
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57 lds2_indexer -db lds -source .
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58 sqlite3 ./lds "SELECT txt_id FROM seq_id WHERE orig=1 AND int_id IS NULL;" > output/swiss_prot_ids
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59 """
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60 stub:
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61 """
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62 mkdir -p output
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63 touch output/swiss_prot_ids
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64 """
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65 }
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66
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67 process run_diamond_egap {
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68 input:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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69 path gnomon_prot_ids
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70 path swiss_prot_ids
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71 path gnomon_prot_asn, stageAs: 'indexed/*'
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72 path swiss_prot_asn, stageAs: 'indexed/*'
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73 val params
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74 output:
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75 path "output/*"
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76 script:
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77 // print(params)
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78 """
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79
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80 ###diamond_bin=`which diamond`
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81 #diamond_egap uses GP_HOME to build paths to both some gp apps, and third-party
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82 #GP_HOME needs to be the directory that contains third-party, and the directory that contains bin/<gp apps>
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83 diamond_bin=\${GP_HOME}/third-party/diamond/diamond
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85 mkdir -p ./asncache/
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87 prime_cache -cache ./asncache/ -ifmt asnb-seq-entry -i ${gnomon_prot_asn} -oseq-ids /dev/null -split-sequences
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88 prime_cache -cache ./asncache/ -ifmt asnb-seq-entry -i ${swiss_prot_asn} -oseq-ids /dev/null -split-sequences
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89
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90 mkdir ./output
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91 mkdir ./work
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92
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93 echo ${params}
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94 echo "${gnomon_prot_ids.join('\n')}" > query.mft
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95 diamond_egap ${params} -asn-cache ./asncache/ -nogenbank -query-manifest query.mft -subject ${swiss_prot_ids} \
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96 -output-dir ./output/ -work-area ./work/ -diamond-executable \${diamond_bin}
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97 rm -rf ./work
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98 """
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99
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100 stub:
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101 """
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102 mkdir -p output
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103 touch output/diamond_output.asn
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104 """
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105 }
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106
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107