Mercurial > repos > fubar > egapx_runner

annotate nf/subworkflows/ncbi/gnomon/gnomon_wnode/main.nf @ 5:6effccc966d0 draft

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planemo upload for repository https://github.com/ncbi/egapx commit 9e59da535540cb4d5c1c412bb2b0969744dfb0b0
author fubar
date Sun, 04 Aug 2024 01:59:37 +0000
parents d9c5c5b87fec
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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 include { merge_params } from '../../utilities'
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5
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6
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7 workflow gnomon_wnode {
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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8 take:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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9 scaffolds
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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10 chains
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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11 chains_slices
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12 hmm_params
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13 softmask_lds2
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14 softmask_lds2_source
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15 genome
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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16 proteins
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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17 parameters // Map : extra parameter and parameter update
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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18 main:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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19 String gpx_qsubmit_params = merge_params("", parameters, 'gpx_qsubmit')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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20 String annot_params = merge_params("-margin 1000 -mincont 1000 -minlen 225 -mpp 10.0 -ncsp 25 -window 200000 -nonconsens -open", parameters, 'annot_wnode')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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21 String gpx_qdump_params = merge_params("-slices-for affinity -sort-by affinity", parameters, 'gpx_qdump')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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22
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23 def (jobs, lines_per_file) = gpx_qsubmit(scaffolds, chains, chains_slices, gpx_qsubmit_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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24 def annot_files = annot(jobs.flatten(), chains, hmm_params, softmask_lds2, softmask_lds2_source, genome, proteins, lines_per_file, annot_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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25 gpx_qdump(annot_files.collect(), gpx_qdump_params)
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26 emit:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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27 outputs = gpx_qdump.out.outputs
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28 }
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29
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30
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31 process gpx_qsubmit {
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32 input:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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33 path scaffolds
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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34 path chains
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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35 path chains_slices
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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36 val params
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37 output:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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38 path "job.*"
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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39 env lines_per_file
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40 script:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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41 njobs=16
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42 """
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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43 echo $scaffolds | tr ' ' '\\n' > scaffolds.mft
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44 for file in $chains_slices; do
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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45 echo \$file >> chains_slices.mft
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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46 # remove path from the first line of this file
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47 sed -i -e '1s/\\(.*\\)\\/\\(.*\\)\$/\\2/' \$file
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48 done
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49 gpx_qsubmit $params -ids-manifest scaffolds.mft -slices-manifest chains_slices.mft -o jobs
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50 total_lines=\$(wc -l <jobs)
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51 (( lines_per_file = (total_lines + ${njobs} - 1) / ${njobs} ))
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52 echo total_lines=\$total_lines, lines_per_file=\$lines_per_file
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53 # split -l\$lines_per_file jobs job. -da 3
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54 # Use round robin to distribute jobs across nodes more evenly
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55 if [ \$total_lines -lt $njobs ]; then
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56 effective_njobs=\$total_lines
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57 else
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58 effective_njobs=$njobs
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59 fi
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60 split -nr/\$effective_njobs jobs job. -da 3
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61 """
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62 stub:
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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63 njobs=16
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64 """
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65 for i in {1..$njobs}; do
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66 echo j.\${i} >> jobs
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67 done
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68 split -nr/$njobs jobs job. -da 3
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69 lines_per_file=10
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70 """
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71 }
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72
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73
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74 process annot {
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75 input:
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76 path jobs
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77 path chains // used for staging chain files, referred from jobs
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78 path hmm_params
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79 path softmask_lds2
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80 path softmask
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81 path genome, stageAs: 'indexed/*'
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82 path proteins_asn, stageAs: 'indexed/*'
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83 val lines_per_file
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84 val params
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85 output:
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86 path "output/*"
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87 script:
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88 job_num = jobs.toString().tokenize('.').last().toInteger()
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89 """
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90 njobs=`wc -l <$jobs`
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91 if [ \$njobs -lt 16 ]; then
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92 threads=\$njobs
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93 else
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94 threads=16
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95 fi
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96
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97 lds2=indexed_lds
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98 if [ -n "$softmask_lds2" ]; then
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99 # patch LDS2 to point to the source
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100 files=\$(sqlite3 $softmask_lds2 -cmd "SELECT file_name FROM file" ".exit")
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101 for f in \$files; do
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102 base=\$(basename \$f)
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103 sqlite3 $softmask_lds2 -cmd "UPDATE file SET file_name = '\$base' WHERE file_name = '\$f'" ".exit"
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104 done
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105 lds2+=",$softmask_lds2"
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106 elif [ -n "$softmask" ]; then
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107 mkdir sm_src
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108 mv $softmask ./sm_src/
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109 lds2_indexer -source ./sm_src/ -db softmask_lds2
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110 lds2+=",softmask_lds2"
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111 fi
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112
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113 filename=\$(basename -- "$jobs")
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114 extension="\${filename##*.}"
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115 (( start_job_id = ((10#\$extension) * $lines_per_file) + 1 ))
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116
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117 # make the local LDS of the genomic fasta
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118 lds2_indexer -source indexed -db indexed_lds
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119
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120 # When running multiple jobs on the cluster there is a chance that
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121 # several jobs will run on the same node and thus generate files
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122 # with the same filename. We need to avoid that to be able to stage
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123 # the output files for gpx_make_outputs. We add the job file numeric
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124 # extension as a prefix to the filename.
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125 mkdir interim
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126 annot_wnode $params -nogenbank -lds2 \$lds2 -start-job-id \$start_job_id -workers \$threads -input-jobs $jobs -param $hmm_params -O interim || true
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127 mkdir output
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128 for f in interim/*; do
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129 if [ -f \$f ]; then
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130 mv \$f output/\${extension}_\$(basename \$f)
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131 fi
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132 done
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133 """
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134 stub:
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135 job_num = jobs.toString().tokenize('.').last().toInteger()
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136 """
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137 mkdir -p output
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138 touch output/sample_gnomon_wnode.${job_num}.out
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139 """
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140 }
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141
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142
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143 process gpx_qdump {
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144 input:
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145 path files, stageAs: "inputs/*"
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146 val params
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147 output:
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148 path "*.out", emit: "outputs"
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149 script:
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150 """
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151 gpx_qdump $params -input-path inputs -output gnomon_wnode.out
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152 """
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153 stub:
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154 """
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155 touch gnomon_wnode.out
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156 """
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157 }