Mercurial > repos > fubar > egapx_runner

annotate nf/subworkflows/ncbi/gnomon/chainer_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
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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
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2 nextflow.enable.dsl=2
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5 include { merge_params } from '../../utilities'
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6 include { run_align_sort } from '../../default/align_sort_sa/main.nf'
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7
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8 split_count=16
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9
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10
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11 workflow chainer_wnode {
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12 take:
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13 alignments
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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14 hmm_params
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15 evidence_denylist
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16 gap_fill_allowlist
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17 scaffolds
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18 trusted_genes
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19 genome
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20 proteins
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21 parameters // Map : extra parameter and parameter update
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22 main:
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23 String input_sorting = parameters.get('input_aligns_sort', '')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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24 def sort_aligns = alignments
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25 if (!input_sorting.contains("presorted")) {
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26 String align_sort_params = ""
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27 if (input_sorting.contains("merge_only")) {
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28 align_sort_params = "-merge"
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29 }
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30 align_sort_params += " -ifmt seq-align -compression none -k subject,subject_start,-subject_end "
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31 // print(align_sort_params)
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32 sort_aligns = run_align_sort([], [], alignments, align_sort_params).collect()
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33 //sort_aligns = align_sort(alignments, align_sort_params)
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34 }
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35 String submit_chainer_params = merge_params("-minimum-abut-margin 20 -separate-within-introns", parameters, 'submit_chainer')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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36 String chainer_wnode_params = merge_params("", parameters, 'chainer_wnode')
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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37 String gpx_make_outputs_params = merge_params("-default-output-name chains -slices-for affinity -sort-by affinity", parameters, 'gpx_make_outputs')
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38
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39 def (jobs, lines_per_file) = generate_jobs(sort_aligns, submit_chainer_params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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40 def collected = run_chainer(jobs.flatten(), sort_aligns, hmm_params, evidence_denylist, gap_fill_allowlist, scaffolds, trusted_genes, genome, proteins, lines_per_file, chainer_wnode_params) | collect
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41
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42 run_gpx_make_outputs(collected, gpx_make_outputs_params)
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43 emit:
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44 chains = run_gpx_make_outputs.out.chains
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45 chains_slices = run_gpx_make_outputs.out.chains_slices
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46 evidence = run_gpx_make_outputs.out.evidence
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47 evidence_slices = run_gpx_make_outputs.out.evidence_slices
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48 }
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49
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50
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51 process generate_jobs {
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52 input:
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53 path sort_aligns
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54 val params
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55 output:
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56 path "job.*"
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57 env lines_per_file
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58 script:
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59 njobs=split_count
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60 """
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61 #!/usr/bin/env bash
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62 # generate_jobs $sort_aligns $params -output chains -output-slices chains_slices -output-evidence evidence -output-evidence-slices evidence_slices
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63 submit_chainer $params -asn $sort_aligns -o jobs
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64 total_lines=\$(wc -l <jobs)
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65 (( lines_per_file = (total_lines + ${njobs} - 1) / ${njobs} ))
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66 echo total_lines=\$total_lines, lines_per_file=\$lines_per_file
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67 ####split -l\$lines_per_file jobs job. -da 3
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68 # Use round robin to distribute jobs across nodes more evenly
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69 if [ \$total_lines -lt $njobs ]; then
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70 effective_njobs=\$total_lines
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71 else
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72 effective_njobs=$njobs
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73 fi
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74 split -nr/\$effective_njobs jobs job. -da 3
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75 """
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76 stub:
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77 """
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78 for i in {1..$split_count}; do
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79 echo "<job query =\\\"lcl|${sort_aligns}:\${i}-\${i}\\\"></job>" >> jobs
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80 done
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81 split -nr/$split_count jobs job. -da 3
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82 lines_per_file=10
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83 """
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84 }
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85
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86
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87 process run_chainer {
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88 input:
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89 path job
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90 path alignments
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91 path hmm_params
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92 path evidence_denylist
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93 path gap_fill_allowlist
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94 path scaffolds
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95 path trusted_genes
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96 path genome, stageAs: 'indexed/*'
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97 path proteins_asn, stageAs: 'indexed/*'
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98 val lines_per_file
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99 val params
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100 output:
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101 path "output/*"
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102 script:
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103 job_num = job.toString().tokenize('.').last().toInteger()
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104 """
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105 echo "${evidence_denylist.join('\n')}" > evidence_denylist.mft
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106 echo "${gap_fill_allowlist.join('\n')}" > gap_fill_allowlist.mft
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107 echo "${scaffolds.join('\n')}" > scaffolds.mft
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108 echo "${trusted_genes.join('\n')}" > trusted_genes.mft
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109 # HACK: derive start_job_id from job file extension
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110 filename=\$(basename -- "$job")
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111 extension="\${filename##*.}"
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112 (( start_job_id = ((10#\$extension) * $lines_per_file) + 1 ))
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113
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114 # make the local LDS of the genomic and protein (if present) sequences
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115 lds2_indexer -source indexed -db LDS2
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116
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117 # When running multiple jobs on the cluster there is a chance that
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118 # several jobs will run on the same node and thus generate files
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119 # with the same filename. We need to avoid that to be able to stage
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120 # the output files for gpx_make_outputs. We add the job file numeric
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121 # extension as a prefix to the filename.
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122 mkdir interim
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123 chainer_wnode $params -start-job-id \$start_job_id -workers 32 -input-jobs ${job} -O interim -nogenbank -lds2 LDS2 -evidence-denylist-manifest evidence_denylist.mft -gap-fill-allowlist-manifest gap_fill_allowlist.mft -param ${hmm_params} -scaffolds-manifest scaffolds.mft -trusted-genes-manifest trusted_genes.mft
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124 mkdir output
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125 for f in interim/*; do
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126 if [ -f \$f ]; then
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127 mv \$f output/\${extension}_\$(basename \$f)
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128 fi
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129 done
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130 """
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131
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132 stub:
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133 job_num = job.toString().tokenize('.').last().toInteger()
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134 """
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135 mkdir -p output
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136 touch output/sample_chainer_wnode.${job_num}.out
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137 """
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138 }
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139
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140
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141 process run_gpx_make_outputs {
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142 input:
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143 path files, stageAs: "gpx_inputs/*"
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144 val params
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145 output:
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146 path "output/chains.*.out.gz", emit: 'chains'
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147 path "output/chains.*.out.gz.slices", emit: 'chains_slices'
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148 path "output/evidence.*.out.gz", emit: 'evidence', optional: true
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149 path "output/evidence.*.out.gz.slices", emit: 'evidence_slices', optional: true
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150 script:
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151 """
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152 ls -1 gpx_inputs/* > gpx_inputs.mft
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153 mkdir -p output
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154 gpx_make_outputs $params -input-manifest gpx_inputs.mft -output output/@.#.out.gz -output-manifest output/@.mft -slices-manifest output/@_slices.mft -num-partitions $split_count
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155 """
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156 stub:
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157 """
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158 mkdir -p output
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159 echo ${files}
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160 for i in {1..$split_count}; do
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161 touch output/chains.\$i.out.gz
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162 touch output/chains.\$i.out.gz.slices
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163 touch output/evidence.\$i.out.gz
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164 touch output/evidence.\$i.out.gz.slices
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165 done
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166 """
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167 }