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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 // rnaseq short EGAPx execution
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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3 // route data to tasks
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5 nextflow.enable.dsl=2
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7 include { sra_query } from './sra_qry/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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8 include { fetch_sra_fasta } from './fetch_sra_fasta/main'
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9 include { star_index } from './star_index/main'
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10 include { star_wnode as star } from './star_wnode/main'
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11 include { bam_strandedness } from './bam_strandedness/main'
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12 include { bam_bin_and_sort } from './bam_bin_and_sort/main'
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13 include { bam2asn } from './convert_from_bam/main'
d9c5c5b87fec planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
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14 include { rnaseq_collapse } from './rnaseq_collapse/main'
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16 params.intermediate = false
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19 workflow rnaseq_short_plane {
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20 take:
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21 genome_asn
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22 scaffolds
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23 unpacked_genome_fasta
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25 // Alternative groups of parameters, one of them should be set
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26 // reads_query - SRA query in the form accepted by NCBI
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27 // reads_ids - list of SRA IDs
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28 // reads, reads_metadata - path to reads accompanied by metadata
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29 reads_query // SRA query
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30 reads_ids // list of SRA IDs
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31 reads // path to reads
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32 reads_metadata // path to reads metadata 13 tab-delimited fields, 1-st - SRA ID, 3-rd paired or unpaired, everything else - not used, but must be present
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33 // 4, 5, 13 - numbers, 5 - non zero number
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34 organelles // path to organelle list
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35 // Alternative parameters, one of them should be set
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36 // tax_id - NCBI tax id of the closest taxon to the genome
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37 // hmm_params - HMM parameters
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38 tax_id // NCBI tax id of the closest taxon to the genome
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39 max_intron // max intron length
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40 task_params // task parameters for every task
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41 main:
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42 // Satisfy quirks of Nextflow compiler
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43 def reads_query1 = reads_query
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44 def reads_ids1 = reads_ids
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45 def ch_reads = Channel.fromList(reads)
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46 // Conditional code on SRA reads source
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47 if (reads_query || reads_ids || reads) {
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48 def index = star_index(unpacked_genome_fasta, task_params.get('star_index', [:]))
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49 def ch_align, ch_align_index, sra_metadata, sra_run_list
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50 if (reads_query || reads_ids) {
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51 def query = reads_query1 ? reads_query1 : reads_ids1.join("[Accession] OR ") + "[Accession]"
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52 (sra_metadata, sra_run_list) = sra_query(query, task_params.get('sra_qry', [:]))
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53 def reads_fasta_pairs = fetch_sra_fasta(sra_run_list, task_params.get('fetch_sra_fasta', [:]))
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54 (ch_align, ch_align_index) = star(scaffolds, reads_fasta_pairs, genome_asn, index, max_intron, task_params.get('star_wnode', [:]))
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55 } else {
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56 sra_metadata = reads_metadata
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57 (ch_align, ch_align_index) = star(scaffolds, ch_reads, genome_asn, index, max_intron, task_params.get('star_wnode', [:]))
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58 }
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59 //
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60
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61 bam_strandedness(ch_align.collect(), sra_metadata, task_params.get('bam_strandedness', [:]))
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62 def strandedness = bam_strandedness.out.strandedness
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64 // Run bam_bin_and_sort
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65 bam_bin_and_sort(ch_align, ch_align_index, unpacked_genome_fasta, organelles, task_params.get('bam_bin_and_sort', [:]))
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66 def bam_bins = bam_bin_and_sort.out.sorted
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68 // Run BAM2ASN
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69 bam2asn(bam_bins, strandedness, genome_asn, task_params.get('convert_from_bam', [:]))
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70 def asn_align = bam2asn.out.align.collect()
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71 def keylist = bam2asn.out.keylist.collect()
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72
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73 rnaseq_collapse(genome_asn, keylist, asn_align, sra_metadata, 10, task_params.get('rnaseq_collapse', [:]))
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74 }
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75
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76 emit:
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77 rnaseq_alignments = rnaseq_collapse.out.alignments
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78 }