diff nf/subworkflows/ncbi/gnomon/locus_link/main.nf @ 0:d9c5c5b87fec draft

planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nf/subworkflows/ncbi/gnomon/locus_link/main.nf	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,116 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+include { merge_params } from '../../utilities'
+
+workflow locus_link {
+    take:
+        best_refseq_prot_hit
+        orthologs
+        annotation 
+        gencoll_asn
+        gnomon_lds2_source
+        best_prot_hit
+        track_loci
+        comparisons
+        curr_prev_compare
+        gnomon_biotypes
+        lxr_data
+        proteins_asn
+        name_from_ortholog
+        parameters  // Map : extra parameter and parameter update
+    main:
+        default_params = ""
+        effective_params = merge_params(default_params, parameters, 'locus_link')
+        run_locus_link(best_refseq_prot_hit, orthologs, annotation, 
+                 gencoll_asn, gnomon_lds2_source, best_prot_hit, track_loci, comparisons,  curr_prev_compare,  
+                 gnomon_biotypes, lxr_data, proteins_asn, name_from_ortholog,  default_params)
+    emit:
+        best_gnomon_prot_hit = run_locus_link.out.best_gnomon_prot_hit
+        best_refseq_prot_hit = run_locus_link.out.best_refseq_prot_hit
+        locustypes = run_locus_link.out.locustypes
+        locus = run_locus_link.out.locus
+        stats = run_locus_link.out.stats
+        all = run_locus_link.out.all
+}
+
+
+
+process run_locus_link {
+    input:
+        path best_refseq_prot_hit
+        path orthologs
+        path annotation 
+        path gencoll_asn
+        path gnomon_lds2_source, stageAs: 'genome/*'
+        path best_prot_hit
+        path track_loci
+        path comparisons
+        path curr_prev_compare
+        path gnomon_biotypes
+        path lxr_data
+        path proteins_asn
+        path name_from_ortholog
+        val parameters
+    output:
+        path ('output/best_gnomon_prot_hit.tsv'), emit: 'best_gnomon_prot_hit'
+        path ('output/best_refseq_prot_hit.tsv'), emit: 'best_refseq_prot_hit'
+        path ('output/locustypes.tsv'), emit: 'locustypes'
+        path ('output/locus.lnk'), emit: 'locus'
+        path ('output/stats.xml'), emit: 'stats'
+        path ('output/*'), emit: 'all'
+    script:
+    """
+    mkdir -p output
+    mkdir -p ./asncache/
+    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i $proteins_asn  -oseq-ids /dev/null -split-sequences
+    
+    lds2_indexer -source genome/ -db LDS2 
+    echo "${best_prot_hit.join('\n')}" > best_prot_hit.mft
+    extract_prot_names -alns best_prot_hit.mft  -nogenbank -o output/best_gnomon_prot_hit.tsv -asn-cache ./asncache/ -lds2 LDS2
+    echo "${best_refseq_prot_hit.join('\n')}" > best_refseq_prot_hit.mft
+    extract_prot_names -alns best_refseq_prot_hit.mft -nogenbank -o output/best_refseq_prot_hit.tsv -asn-cache ./asncache/ -lds2 LDS2 
+    echo "${annotation.join('\n')}" > annotation.mft
+    echo "${curr_prev_compare.join('\n')}" > curr_prev_compare.mft
+    echo  "${comparisons.join('\n')}"  > comparisons.mft
+    str=""
+    if [ ! -z "$orthologs" ]
+    then
+        str="\$str -orthologs $orthologs"
+    fi
+    if [ ! -z "$lxr_data" ]
+    then
+        str="\$str -lxr $lxr_data"
+    else
+        touch lxr_data
+        str="\$str -lxr lxr_data"
+    fi
+
+    if [ ! -z "$track_loci" ]
+    then
+        str="\$str -locus_track $track_loci"
+    else
+        touch track_loci
+        str="\$str -locus_track track_loci"
+    fi
+    if [ ! -z "$name_from_ortholog" ]
+    then
+        str="\$str -name_from_ortholog_rpt $name_from_ortholog"
+    else
+	    touch name_from_ortholog
+        str="\$str -name_from_ortholog_rpt name_from_ortholog"
+    fi
+
+    locus_type  -no_acc_reserve  -annots annotation.mft -gc $gencoll_asn -gnomon_biotype $gnomon_biotypes -o_stats output/stats.xml -o_locustypes output/locustypes.tsv -o_locus_lnk output/locus.lnk  -annotcmp comparisons.mft  -annotcmp_pb curr_prev_compare.mft \$str
+    """
+    stub:
+    """
+    mkdir -p output
+    touch output/best_gnomon_prot_hit.tsv
+    touch output/best_refseq_prot_hit.tsv
+    touch output/locustypes.tsv
+    touch output/locus.lnk
+    touch output/stats.xml
+    """
+}
+