kkonganti@0: // Define any required imports for this specific workflow
kkonganti@0: import java.nio.file.Paths
kkonganti@0: import java.util.zip.GZIPInputStream
kkonganti@0: import java.io.FileInputStream
kkonganti@0: import nextflow.file.FileHelper
kkonganti@0: 
kkonganti@0: 
kkonganti@0: // Include any necessary methods
kkonganti@0: include { \
kkonganti@0:     summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
kkonganti@0:     addPadding; wrapUpHelp           } from "${params.routines}"
kkonganti@0: include { fastpHelp                  } from "${params.toolshelp}${params.fs}fastp"
kkonganti@0: include { kmaalignHelp               } from "${params.toolshelp}${params.fs}kmaalign"
kkonganti@0: include { seqkitgrepHelp             } from "${params.toolshelp}${params.fs}seqkitgrep"
kkonganti@0: include { salmonidxHelp              } from "${params.toolshelp}${params.fs}salmonidx"
kkonganti@0: include { sourmashsketchHelp         } from "${params.toolshelp}${params.fs}sourmashsketch"
kkonganti@0: include { sourmashgatherHelp         } from "${params.toolshelp}${params.fs}sourmashgather"
kkonganti@0: include { sfhpyHelp                  } from "${params.toolshelp}${params.fs}sfhpy"
kkonganti@0: include { gsalkronapyHelp            } from "${params.toolshelp}${params.fs}gsalkronapy"
kkonganti@0: include { kronaktimporttextHelp      } from "${params.toolshelp}${params.fs}kronaktimporttext"
kkonganti@0: 
kkonganti@0: // Exit if help requested before any subworkflows
kkonganti@0: if (params.help) {
kkonganti@0:     log.info help()
kkonganti@0:     exit 0
kkonganti@0: }
kkonganti@0: 
kkonganti@0: 
kkonganti@0: // Include any necessary modules and subworkflows
kkonganti@0: include { PROCESS_FASTQ           } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@0: include { FASTP                   } from "${params.modules}${params.fs}fastp${params.fs}main"
kkonganti@0: include { KMA_ALIGN               } from "${params.modules}${params.fs}kma${params.fs}align${params.fs}main"
kkonganti@0: include { OTF_GENOME              } from "${params.modules}${params.fs}otf_genome${params.fs}main"
kkonganti@0: include { SEQKIT_GREP             } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
kkonganti@0: include { SALMON_INDEX            } from "${params.modules}${params.fs}salmon${params.fs}index${params.fs}main"
kkonganti@0: include { SALMON_QUANT            } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
kkonganti@0: include { SOURMASH_SKETCH         } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
kkonganti@0: include { SOURMASH_SKETCH \
kkonganti@0:     as REDUCE_DB_IDX              } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
kkonganti@0: include { SOURMASH_GATHER         } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
kkonganti@0: include { NOWAYOUT_RESULTS        } from "${params.modules}${params.fs}nowayout_results${params.fs}main"
kkonganti@0: include { KRONA_KTIMPORTTEXT      } from "${params.modules}${params.fs}krona${params.fs}ktimporttext${params.fs}main"
kkonganti@0: include { DUMP_SOFTWARE_VERSIONS  } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@0: include { MULTIQC                 } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL WORKFLOW
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: def reads_platform = 0
kkonganti@0: reads_platform += (params.input ? 1 : 0)
kkonganti@0: 
kkonganti@0: if (reads_platform < 1 || reads_platform == 0) {
kkonganti@0:     stopNow("Please mention at least one absolute path to input folder which contains\n" +
kkonganti@0:             "FASTQ files sequenced using the --input option.\n" +
kkonganti@0:         "Ex: --input (Illumina or Generic short reads in FASTQ format)")
kkonganti@0: }
kkonganti@0: 
kkonganti@0: params.fastp_adapter_fasta ? checkMetadataExists(params.fastp_adapter_fasta, 'Adapter sequences FASTA') : null
kkonganti@0: checkMetadataExists(params.lineages_csv, 'Lineages CSV')
kkonganti@0: checkMetadataExists(params.kmaalign_idx, 'KMA Indices')
kkonganti@0: checkMetadataExists(params.ref_fna, 'FASTA reference')
kkonganti@0: 
kkonganti@0: ch_sourmash_lin = file( params.lineages_csv )
kkonganti@0: 
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     RUN THE BETTERCALLSAL WORKFLOW
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: workflow NOWAYOUT {
kkonganti@0:     main:
kkonganti@0:         log.info summaryOfParams()
kkonganti@0: 
kkonganti@0:         PROCESS_FASTQ()
kkonganti@0: 
kkonganti@0:         PROCESS_FASTQ.out.versions
kkonganti@0:             .set { software_versions }
kkonganti@0: 
kkonganti@0:         PROCESS_FASTQ.out.processed_reads
kkonganti@0:             .set { ch_processed_reads }
kkonganti@0: 
kkonganti@0:         ch_processed_reads
kkonganti@0:             .map { meta, fastq ->
kkonganti@0:                 meta.get_kma_hit_accs = true
kkonganti@0:                 meta.salmon_decoys = params.dummyfile
kkonganti@0:                 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
kkonganti@0:                 meta.kma_t_db = params.kmaalign_idx
kkonganti@0:                 [ meta, fastq ]
kkonganti@0:             }
kkonganti@0:             .filter { meta, fastq ->
kkonganti@0:                 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
kkonganti@0:                 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toAbsolutePath().toString() ) )
kkonganti@0:                 fq_gzip.read() != -1
kkonganti@0:             }
kkonganti@0:             .set { ch_processed_reads }
kkonganti@0: 
kkonganti@0:         FASTP( ch_processed_reads )
kkonganti@0: 
kkonganti@0:         FASTP.out.json
kkonganti@0:             .map { meta, json ->
kkonganti@0:                 json
kkonganti@0:             }
kkonganti@0:             .collect()
kkonganti@0:             .set { ch_multiqc }
kkonganti@0: 
kkonganti@0:         KMA_ALIGN(
kkonganti@0:             FASTP.out.passed_reads
kkonganti@0:                 .map { meta, fastq ->
kkonganti@0:                     [meta, fastq, []]
kkonganti@0:                 }
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         OTF_GENOME(
kkonganti@0:             KMA_ALIGN.out.hits
kkonganti@0:                 .join(KMA_ALIGN.out.frags)
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         OTF_GENOME.out.reads_extracted
kkonganti@0:             .filter { meta, fasta ->
kkonganti@0:                 fa_file = ( fasta.getClass().toString() =~ /ArrayList/ ? fasta : [ fasta ] )
kkonganti@0:                 fa_gzip = new GZIPInputStream( new FileInputStream( fa_file[0].toAbsolutePath().toString() ) )
kkonganti@0:                 fa_gzip.read() != -1
kkonganti@0:             }
kkonganti@0:             .set { ch_mito_aln_reads }
kkonganti@0: 
kkonganti@0:         SEQKIT_GREP(
kkonganti@0:             KMA_ALIGN.out.hits
kkonganti@0:                 .filter { meta, mapped_refs ->
kkonganti@0:                     patterns = file( mapped_refs )
kkonganti@0:                     patterns.size() > 0
kkonganti@0:                 }
kkonganti@0:                 .map { meta, mapped_refs ->
kkonganti@0:                     [meta, params.ref_fna, mapped_refs]
kkonganti@0:                 }
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         SALMON_INDEX( SEQKIT_GREP.out.fastx )
kkonganti@0: 
kkonganti@0:         SALMON_QUANT(
kkonganti@0:             ch_mito_aln_reads
kkonganti@0:                 .join( SALMON_INDEX.out.idx )
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         REDUCE_DB_IDX(
kkonganti@0:             SEQKIT_GREP.out.fastx,
kkonganti@0:             true,
kkonganti@0:             false,
kkonganti@0:             'db'
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         SOURMASH_SKETCH(
kkonganti@0:             ch_mito_aln_reads,
kkonganti@0:             false,
kkonganti@0:             false,
kkonganti@0:             'query'
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         SOURMASH_GATHER(
kkonganti@0:             SOURMASH_SKETCH.out.signatures
kkonganti@0:                 .join( REDUCE_DB_IDX.out.signatures ),
kkonganti@0:                 [], [], [], []
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         // SOURMASH_TAX_METAGENOME(
kkonganti@0:         //     SOURMASH_GATHER.out.result
kkonganti@0:         //         .groupTuple(by: [0])
kkonganti@0:         //         .map { meta, csv ->
kkonganti@0:         //             [ meta, csv, ch_sourmash_lin ]
kkonganti@0:         //         }
kkonganti@0:         // )
kkonganti@0: 
kkonganti@0:         // SOURMASH_TAX_METAGENOME.out.csv
kkonganti@0:         //     .map { meta, csv ->
kkonganti@0:         //         csv
kkonganti@0:         //     }
kkonganti@0:         //     .set { ch_lin_csv }
kkonganti@0: 
kkonganti@0:         // SOURMASH_TAX_METAGENOME.out.tsv
kkonganti@0:         //     .tap { ch_lin_krona }
kkonganti@0:         //     .map { meta, tsv ->
kkonganti@0:         //         tsv
kkonganti@0:         //     }
kkonganti@0:         //     .tap { ch_lin_tsv }
kkonganti@0: 
kkonganti@0:         SOURMASH_GATHER.out.result
kkonganti@0:             .groupTuple(by: [0])
kkonganti@0:             .map { meta, csv ->
kkonganti@0:                 [ csv ]
kkonganti@0:             }
kkonganti@0:             .concat(
kkonganti@0:                 SALMON_QUANT.out.results
kkonganti@0:                     .map { meta, salmon_res ->
kkonganti@0:                         [ salmon_res ]
kkonganti@0:                     }
kkonganti@0:             )
kkonganti@0:             .concat(
kkonganti@0:                 SOURMASH_GATHER.out.failed
kkonganti@0:                     .map { meta, failed ->
kkonganti@0:                         [ failed ]
kkonganti@0:                     }
kkonganti@0:             )
kkonganti@0:             .concat( OTF_GENOME.out.failed )
kkonganti@0:             .collect()
kkonganti@0:             .flatten()
kkonganti@0:             .collect()
kkonganti@0:             .set { ch_gene_abn }
kkonganti@0:         
kkonganti@0:         NOWAYOUT_RESULTS( ch_gene_abn, ch_sourmash_lin )
kkonganti@0: 
kkonganti@0:         NOWAYOUT_RESULTS.out.tsv
kkonganti@0:             .flatten()
kkonganti@0:             .filter { tsv -> tsv.toString() =~ /.*${params.krona_res_suffix}$/ }
kkonganti@0:             .map { tsv ->
kkonganti@0:                     meta = [:]
kkonganti@0:                     meta.id = "${params.cfsanpipename}_${params.pipeline}_krona"
kkonganti@0:                     [ meta, tsv ]
kkonganti@0:             }
kkonganti@0:             .groupTuple(by: [0])
kkonganti@0:             .set { ch_lin_krona }
kkonganti@0: 
kkonganti@0:         // ch_lin_tsv
kkonganti@0:         //     .mix( ch_lin_csv )
kkonganti@0:         //     .collect()
kkonganti@0:         //     .set { ch_lin_summary }
kkonganti@0: 
kkonganti@0:         // SOURMASH_TAX_METAGENOME.out.txt
kkonganti@0:         //     .map { meta, txt ->
kkonganti@0:         //         txt
kkonganti@0:         //     }
kkonganti@0:         //     .collect()
kkonganti@0:         //     .set { ch_lin_kreport }
kkonganti@0: 
kkonganti@0:         // NOWAYOUT_RESULTS(
kkonganti@0:         //     ch_lin_summary
kkonganti@0:         //         .concat( SOURMASH_GATHER.out.failed )
kkonganti@0:         //         .concat( OTF_GENOME.out.failed )
kkonganti@0:         //         .collect()
kkonganti@0:         // )
kkonganti@0: 
kkonganti@0:         KRONA_KTIMPORTTEXT( ch_lin_krona )
kkonganti@0:         
kkonganti@0:         DUMP_SOFTWARE_VERSIONS(
kkonganti@0:             software_versions
kkonganti@0:                 .mix (
kkonganti@0:                     FASTP.out.versions,
kkonganti@0:                     KMA_ALIGN.out.versions,
kkonganti@0:                     SEQKIT_GREP.out.versions,
kkonganti@0:                     REDUCE_DB_IDX.out.versions,
kkonganti@0:                     SOURMASH_SKETCH.out.versions,
kkonganti@0:                     SOURMASH_GATHER.out.versions,
kkonganti@0:                     SALMON_INDEX.out.versions,
kkonganti@0:                     SALMON_QUANT.out.versions,
kkonganti@0:                     NOWAYOUT_RESULTS.out.versions,
kkonganti@0:                     KRONA_KTIMPORTTEXT.out.versions
kkonganti@0:                 )
kkonganti@0:                 .unique()
kkonganti@0:                 .collectFile(name: 'collected_versions.yml')
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         DUMP_SOFTWARE_VERSIONS.out.mqc_yml
kkonganti@0:             .concat(
kkonganti@0:                 ch_multiqc,
kkonganti@0:                 NOWAYOUT_RESULTS.out.mqc_yml
kkonganti@0:             )
kkonganti@0:             .collect()
kkonganti@0:             .flatten()
kkonganti@0:             .collect()
kkonganti@0:             .set { ch_multiqc }
kkonganti@0: 
kkonganti@0:         MULTIQC( ch_multiqc )
kkonganti@0: }
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: workflow.onComplete {
kkonganti@0:     if (workflow.success) {
kkonganti@0:         sendMail()
kkonganti@0:     }
kkonganti@0: }
kkonganti@0: 
kkonganti@0: workflow.onError {
kkonganti@0:     sendMail()
kkonganti@0: }
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     METHOD TO CHECK METADATA EXISTENCE
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: def checkMetadataExists(file_path, msg) {
kkonganti@0:     file_path_obj = file( file_path )
kkonganti@0:     
kkonganti@0:     if (msg.toString().find(/(?i)KMA/)) {
kkonganti@8:         if (!file_path_obj.parent.exists()) {
kkonganti@0:             stopNow("Please check if your ${msg}\n" +
kkonganti@0:                 "[ ${file_path} ]\nexists and that the files are not of size 0.")
kkonganti@0:         }
kkonganti@8:         
kkonganti@8:         // Check if db files within parent path are empty.
kkonganti@8:         file_path_obj.eachFileRecurse {
kkonganti@8:             if (it.size() == 0) {
kkonganti@8:                 stopNow("For ${msg}, within\n" +
kkonganti@8:                 "[ ${file_path} ],\nthe following file is of size 0: ${it.name}")
kkonganti@8:             }
kkonganti@8:         }
kkonganti@8: 
kkonganti@0:     }
kkonganti@0:     else if (!file_path_obj.exists() || file_path_obj.size() == 0) {
kkonganti@0:         stopNow("Please check if your ${msg} file\n" +
kkonganti@0:             "[ ${file_path} ]\nexists and is not of size 0.")
kkonganti@0:     }
kkonganti@0: }
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: def help() {
kkonganti@0: 
kkonganti@0:     Map helptext = [:]
kkonganti@0: 
kkonganti@0:     helptext.putAll (
kkonganti@0:         fastqEntryPointHelp() +
kkonganti@0:         fastpHelp(params).text +
kkonganti@0:         kmaalignHelp(params).text +
kkonganti@0:         seqkitgrepHelp(params).text +
kkonganti@0:         salmonidxHelp(params).text +
kkonganti@0:         sourmashsketchHelp(params).text +
kkonganti@0:         sourmashgatherHelp(params).text +
kkonganti@0:         sfhpyHelp(params).text +
kkonganti@0:         gsalkronapyHelp(params).text +
kkonganti@0:         kronaktimporttextHelp(params).text +
kkonganti@0:         wrapUpHelp()
kkonganti@0:     )
kkonganti@0: 
kkonganti@0:     return addPadding(helptext)
kkonganti@0: }