Mercurial > repos > fubar > egapx_runner
annotate nf/subworkflows/ncbi/target_proteins/main.nf @ 0:d9c5c5b87fec draft
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author | fubar |
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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
fubar
parents:
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1 #!/usr/bin/env nextflow |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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2 // main nextflow script for EGAPx execution |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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3 // route data to subworkflows |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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4 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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5 nextflow.enable.dsl=2 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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6 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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7 include { miniprot } from './miniprot/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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8 include { align_filter_sa } from './align_filter_sa/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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9 include { best_aligned_prot } from './best_aligned_prot/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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10 include { paf2asn } from './paf2asn/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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11 include { run_align_sort} from '../default/align_sort_sa/main' |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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12 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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13 params.intermediate = false |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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14 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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15 |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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16 workflow target_proteins_plane { |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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17 take: |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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18 unpacked_genome_fasta |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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changeset
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19 genome_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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20 gencoll_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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21 unpacked_proteins_fasta |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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22 proteins_asn |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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23 max_intron |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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24 task_params // task parameters for every task |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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changeset
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25 main: |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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26 // Protein alignments |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
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27 miniprot(unpacked_genome_fasta, unpacked_proteins_fasta, max_intron, task_params.get('miniprot', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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28 def miniprot_file = miniprot.out.miniprot_file |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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29 paf2asn(genome_asn, proteins_asn, miniprot_file, task_params.get('paf2asn', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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30 def converted_asn = paf2asn.out.asn_file |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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31 best_aligned_prot(genome_asn, proteins_asn, converted_asn.collect(), gencoll_asn, task_params.get('best_aligned_prot', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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32 align_filter_sa(genome_asn, proteins_asn, best_aligned_prot.out.asn_file, task_params.get('align_filter_sa', [:])) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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33 run_align_sort(genome_asn, proteins_asn,align_filter_sa.out.filtered_file, |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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34 "-k subject,subject_start,-subject_end,subject_strand,query,query_start,-query_end,query_strand,-num_ident,gap_count" ) |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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35 emit: |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
changeset
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36 protein_alignments = run_align_sort.out |
d9c5c5b87fec
planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
fubar
parents:
diff
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37 } |