view nf/subworkflows/ncbi/shared/diamond/main.nf @ 0:d9c5c5b87fec draft

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

#!/usr/bin/env nextflow
nextflow.enable.dsl=2


/*
 *Execution of: 
 * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/diamond 
 *    -asn-cache /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/sequence_cache 
 *    -blastp-args '--sam-query-len --comp-based-stats 0 --evalue 0.0001 --very-sensitive --max-hsps 3' 
 *    -diamond-executable /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/third-party/diamond/diamond 
 *    -lds2 /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/prot_gnomon_prepare.8202002/out/LDS2 
 *    -ofmt seq-align-set 
 *    -output-dir /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out 
 *    -output-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out/align.mft 
 *    -output-prefix hits 
 *    ## query is gnomon-made proteins 'gnl|GNOMON|23016146.p'
 *    ## query-fmt is <String, `fasta', `seq-ids'>
 *    -query-fmt seq-ids 
 *    -query-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/query_ids.mft 
 *    ## subject is swiss-prot ids 'sp|A0A009IHW8.1|ABTIR_ACIB9'
 *    -subject-fmt seq-ids 
 *    -subject-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/subject_ids.mft 
 *    -work-area /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/tmp

 */

include {to_map; shellSplit } from '../../utilities'


swiss_prot_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/reference_sets/swissprot.asnb.gz'
process fetch_swiss_prot_asn  {
    input:
    output:
        path "output/swissprot.asnb", emit: "swiss_prot_asn"
    script:
    """
        curl -O '$swiss_prot_url'
        gunzip swissprot.asnb.gz
        mkdir -p output
        mv swissprot.asnb output/swissprot.asnb
    """   
    stub:
    """
        mkdir -p output
        touch output/swissprot.asnb
    """
}

process get_swiss_prot_ids {
    input:
        path swiss_prot_asn
    output:
        path "output/swiss_prot_ids"
    script: 
    """
        mkdir -p output
        lds2_indexer  -db lds -source  .
        sqlite3 ./lds "SELECT txt_id FROM seq_id WHERE orig=1 AND int_id IS NULL;"    > output/swiss_prot_ids
    """
    stub:
    """
        mkdir -p output
        touch output/swiss_prot_ids
    """
}

process run_diamond_egap {
    input:
        path gnomon_prot_ids
        path swiss_prot_ids
        path gnomon_prot_asn, stageAs: 'indexed/*'
        path swiss_prot_asn, stageAs: 'indexed/*'
        val params
    output:
        path "output/*"
    script:
    // print(params)
    """
   
    ###diamond_bin=`which diamond`
    #diamond_egap uses GP_HOME to build paths to both some gp apps, and third-party
    #GP_HOME needs to be the directory that contains third-party, and the directory that contains bin/<gp apps> 
    diamond_bin=\${GP_HOME}/third-party/diamond/diamond
    
    mkdir -p ./asncache/

    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${gnomon_prot_asn} -oseq-ids /dev/null -split-sequences
    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${swiss_prot_asn} -oseq-ids /dev/null -split-sequences

    mkdir ./output
    mkdir ./work

    echo  ${params}
    echo "${gnomon_prot_ids.join('\n')}" > query.mft
    diamond_egap  ${params} -asn-cache ./asncache/ -nogenbank -query-manifest query.mft -subject ${swiss_prot_ids} \
        -output-dir ./output/ -work-area ./work/  -diamond-executable \${diamond_bin}
    rm -rf ./work
    """

    stub:
    """
    mkdir -p output
    touch output/diamond_output.asn
    """
}