Mercurial > repos > fubar > egapx_runner

annotate nf/subworkflows/ncbi/default/annot_builder/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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4 include { merge_params } from '../../utilities'
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6 // annot_builder_main collection_dir ${output}/COLLECTION accept_dir ${output}/ACCEPT conflict_dir ${output}/CONFLICT report_dir ${output}/REPORT test_dir ${output}/TEST i
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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7 // reftrack_attrs_manifest ${input.reftrack_attrs} loss_pct_ccds 0.0 loss_pct_refseq_ref_primary 1.0 loss_pct_refseq_alt_ref_loci 100.0 loss_pct_refseq_patches 100.0 loss_pct_refseq_other 1.0
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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8 // annot_builder_input name gnomon desc Gnomon aliases Gnomon|Chainer|PartAbInitio|FullAbInitio|Chainer_GapFilled|PartAbInitio_GapFilled
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9 // is_primary 1 input_manifest ${input.gnomon_models} model_maker gnomon2model use_secondary_support 1 keep_top_N_models 50
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10 // drop_alt_brs_overlap 1 merge_variants 1 enable_AR0050_AR0048 1 max_pct_ab_initio 50
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11 // annot_builder -accept-output both -asn-cache ${GP_cache_dir} -conffile ${conffile} -gc-assembly-manifest ${input.gencoll_asn} -logfile ${logfile}
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13 // not implimented, future examples
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14 //load_annot_builder_tracking_data -stats-xml ${output}/REPORT/stats.xml -taskrun ${taskrun.id}
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15 //annot_builder_input name bestrs desc BestRefSeq is_primary 1 input_manifest ${input.best_rs_seqalign} model_maker splign2model user_filter lxr_data.is_refseq=1
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16 //annot_builder_input name ng desc Curated Genomic is_primary 1 input_manifest ${input.best_ng_seqalign} model_maker ng2model score_filter rank=1 exclude_subtypes CloneRef,misc_difference,STS,tRNA,variation,VariationRef exclude_types Biosrc,Pub
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17 //annot_builder_input name imgt desc IMGT is_primary 1 input_manifest ${input.imgt} model_maker imgt2model use_secondary_support 0
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18 //annot_builder_input name rfam desc cmsearch aliases Rfam is_primary 1 input_manifest ${input.rfam} model_maker gnomon2model
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19 //annot_builder_input name trna desc tRNAscan-SE is_primary 1 input_manifest ${input.trna_annot} model_maker passthru
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20 //annot_builder_input name blessed desc SelectedGeneRepresentative is_primary 0 input_manifest ${input.best_rs_seqalign} model_maker splign2model score_filter rank=1 user_filter lxr_data.is_refseq=0
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22 workflow annot_builder {
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23 take:
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24 gencoll_asn
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25 gnomon_file
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26 genome_asn
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27 parameters // Map : extra parameter and parameter update
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28 main:
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30 def m = annot_builder_main('outdir', params).collect()
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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31 def i = annot_builder_input('outdir', m, '01', gnomon_file, params)
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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32 // FIXME: intended params 4-5 to be lists of all input files and all input manifests, but it complained with only one entry
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33 def (all, accept, accept_ftable, annot) = annot_builder_run('outdir', i[0], gencoll_asn, i[1], gnomon_file, genome_asn, params)
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35 emit:
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36 outputs = all
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37 accept_asn = accept
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38 accept_ftable_annot = accept_ftable
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39 annot_files = annot
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40 }
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41
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43 // [Main]
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44 // accept_dir = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/out/ACCEPT"
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45 // collection_dir = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/out/COLLECTION"
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46 // conflict_dir = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/out/CONFLICT"
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47 // loss_pct_ccds = "0.0"
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48 // loss_pct_refseq_alt_ref_loci = "100.0"
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49 // loss_pct_refseq_other = "1.0"
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50 // loss_pct_refseq_patches = "100.0"
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51 // loss_pct_refseq_ref_primary = "1.0"
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52 // reftrack_attrs_manifest = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/inp/reftrack_attrs.mft"
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53 // report_dir = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/out/REPORT"
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54 // test_dir = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/out/TEST"
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55
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56 process annot_builder_main {
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57 input:
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58 val outdir
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59 val params
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60 output:
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61 path "annot_builder_main.ini"
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62 script:
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63 """
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64 #!/usr/bin/env python3
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65 with open('annot_builder_main.ini', 'w') as outf:
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66 print('[Main]', file=outf)
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67 print('accept_dir = "$outdir/ACCEPT"', file=outf)
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68 print('collection_dir = "$outdir/COLLECTION"', file=outf)
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69 print('conflict_dir = "$outdir/CONFLICT"', file=outf)
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70 print('loss_pct_ccds = "0.0"', file=outf)
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71 print('loss_pct_refseq_alt_ref_loci = "100.0"', file=outf)
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72 print('loss_pct_refseq_other = "1.0"', file=outf)
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73 print('loss_pct_refseq_patches = "100.0"', file=outf)
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74 print('loss_pct_refseq_ref_primary = "1.0"', file=outf)
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75 print('report_dir = "$outdir/REPORT"', file=outf)
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76 print('test_dir = "$outdir/TEST"', file=outf)
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77 """
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78 stub:
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79 """
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80 touch annot_builder_main.ini
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81 echo 'main' > annot_builder_main.ini
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82 """
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83 }
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84
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85
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86 // [DataProvider06]
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87 // aliases = "Gnomon|Chainer|PartAbInitio|FullAbInitio|Chainer_GapFilled|PartAbInitio_GapFilled"
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88 // desc = "Gnomon"
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89 // drop_alt_brs_overlap = "1"
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90 // enable_AR0050_AR0048 = "1"
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91 // input_manifest = "/netmnt/vast01/gpi/prod/GPIPE_PROD/data00/Lagenorhynchus_albirostris/1.1.470794/6389647/annot_builder.46361542/inp/gnomon_models.mft"
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92 // is_primary = "1"
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93 // keep_top_N_models = "50"
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94 // max_pct_ab_initio = "50"
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95 // merge_variants = "1"
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96 // model_maker = "gnomon2model"
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97 // name = "gnomon"
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98 // use_secondary_support = "1"
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99
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100 process annot_builder_input {
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101 input:
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102 val outdir
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103 path prior_file
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104 val provider_number
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105 path input_file
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106 val params
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107 output:
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108 path("annot_builder_input.ini")
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109 path("input_manifest_${provider_number}.mft")
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110 script:
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111 """
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112 #!/usr/bin/env python3
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113 with open('annot_builder_input.ini', 'w') as outf:
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114
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115 with open('${prior_file}', 'r') as f:
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116 print(f.read(), file=outf)
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117
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118 print('[DataProvider${provider_number}]', file=outf)
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119
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120 im = 'input_manifest_${provider_number}.mft'
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121 inpf = '${input_file}'
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122 with open(im, 'w') as mft:
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123 print(inpf, file=mft)
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124 print(f'input_manifest="{im}"', file=outf)
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125
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126 print('aliases = "Gnomon|Chainer|PartAbInitio|FullAbInitio|Chainer_GapFilled|PartAbInitio_GapFilled"', file=outf)
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127 print('desc = "Gnomon"', file=outf)
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128 print('name = "gnomon"', file=outf)
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129 print('model_maker = "gnomon2model"', file=outf)
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130
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131 print('drop_alt_brs_overlap = "1"', file=outf)
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132 print('enable_AR0050_AR0048 = "1"', file=outf)
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133 print('is_primary = "1"', file=outf)
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134 print('keep_top_N_models = "50"', file=outf)
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135 print('max_pct_ab_initio = "50"', file=outf)
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136 print('merge_variants = "1"', file=outf)
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137 print('use_secondary_support = "1"', file=outf)
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138 """
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139 stub:
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140 """
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141 touch annot_builder_input.ini
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142 touch input_manifest_${provider_number}.mft
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143 cp ${prior_file} annot_builder_input.ini
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144 echo 'input ${provider_number}' >> annot_builder_input.ini
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145 """
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146 }
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147
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148
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149 // ## annot_builder -accept-output both -asn-cache ${GP_cache_dir} -conffile ${conffile} -gc-assembly-manifest ${input.gencoll_asn} -logfile ${logfile}
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150 process annot_builder_run {
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151 input:
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152 val outdir
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153 path conffile, stageAs: 'annot_builder_final.ini'
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154 path gencoll_asn
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155 path input_manifests
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156 path input_files
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157 path genome_asn, stageAs: 'genome/*'
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158 val params
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159 output:
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160 path "${outdir}/*", emit: "all"
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161 path "${outdir}/ACCEPT/accept.asn", emit: "accept", optional: true
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162 path "${outdir}/ACCEPT/accept.ftable_annot", emit: "accept_ftable_annot", optional: true
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163 path "${outdir}/ACCEPT/*.annot", optional: true
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164 script:
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165 """
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166 mkdir -p $outdir/ACCEPT
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167 mkdir -p $outdir/COLLECTION
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168 mkdir -p $outdir/CONFLICT
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169 mkdir -p $outdir/REPORT
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170 mkdir -p $outdir/TEST
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171
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172 lds2_indexer -source genome/ -db LDS2
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173 # EXCEPTION_STACK_TRACE_LEVEL=Warning DEBUG_STACK_TRACE_LEVEL=Warning DIAG_POST_LEVEL=Trace
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174 annot_builder -accept-output both -nogenbank -lds2 LDS2 -conffile $conffile -gc-assembly $gencoll_asn -logfile ${outdir}/annot_builder.log
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175 cat ${outdir}/ACCEPT/*.ftable.annot > ${outdir}/ACCEPT/accept.ftable_annot
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176 """
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177 stub:
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178 """
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179 mkdir -p $outdir/ACCEPT
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180 mkdir -p $outdir/COLLECTION
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181 mkdir -p $outdir/CONFLICT
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182 mkdir -p $outdir/REPORT
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183 mkdir -p $outdir/TEST
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184
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185 echo "1" > ${outdir}/annot_builder.log
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186 echo "2" > ${outdir}/accept.asn
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187 echo "3" > ${outdir}/accept.ftable.annot
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188
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189
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190 echo "4" > ${outdir}/ACCEPT/accept.asn
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191 echo "5" > ${outdir}/ACCEPT/accept.ftable_annot
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192 echo "S1" > ${outdir}/ACCEPT/S1.annot
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193 echo "S2" > ${outdir}/ACCEPT/S2.annot
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194
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195 """
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196 }