kkonganti@1: // Define any required imports for this specific workflow
kkonganti@1: import java.nio.file.Paths
kkonganti@1: import java.util.zip.GZIPInputStream
kkonganti@1: import java.io.FileInputStream
kkonganti@1: import nextflow.file.FileHelper
kkonganti@1: 
kkonganti@1: 
kkonganti@1: // Include any necessary methods
kkonganti@1: include { \
kkonganti@1:     summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
kkonganti@1:     addPadding; wrapUpHelp    } from "${params.routines}"
kkonganti@1: include { bbmergeHelp         } from "${params.toolshelp}${params.fs}bbmerge"
kkonganti@1: include { fastpHelp           } from "${params.toolshelp}${params.fs}fastp"
kkonganti@1: include { mashscreenHelp      } from "${params.toolshelp}${params.fs}mashscreen"
kkonganti@1: include { tuspyHelp           } from "${params.toolshelp}${params.fs}tuspy"
kkonganti@1: include { sourmashsketchHelp  } from "${params.toolshelp}${params.fs}sourmashsketch"
kkonganti@1: include { sourmashgatherHelp  } from "${params.toolshelp}${params.fs}sourmashgather"
kkonganti@1: include { sourmashsearchHelp  } from "${params.toolshelp}${params.fs}sourmashsearch"
kkonganti@1: include { sfhpyHelp           } from "${params.toolshelp}${params.fs}sfhpy"
kkonganti@1: include { kmaindexHelp        } from "${params.toolshelp}${params.fs}kmaindex"
kkonganti@1: include { kmaalignHelp        } from "${params.toolshelp}${params.fs}kmaalign"
kkonganti@1: include { salmonidxHelp       } from "${params.toolshelp}${params.fs}salmonidx"
kkonganti@1: include { gsrpyHelp           } from "${params.toolshelp}${params.fs}gsrpy"
kkonganti@1: 
kkonganti@1: // Exit if help requested before any subworkflows
kkonganti@1: if (params.help) {
kkonganti@1:     log.info help()
kkonganti@1:     exit 0
kkonganti@1: }
kkonganti@1: 
kkonganti@1: 
kkonganti@1: // Include any necessary modules and subworkflows
kkonganti@1: include { PROCESS_FASTQ           } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@1: include { CAT_CAT                 } from "${params.modules}${params.fs}cat_cat${params.fs}main"
kkonganti@1: include { FASTQC                  } from "${params.modules}${params.fs}fastqc${params.fs}main"
kkonganti@1: include { BBTOOLS_BBMERGE         } from "${params.modules}${params.fs}bbtools${params.fs}bbmerge${params.fs}main"
kkonganti@1: include { FASTP                   } from "${params.modules}${params.fs}fastp${params.fs}main"
kkonganti@1: include { MASH_SCREEN             } from "${params.modules}${params.fs}mash${params.fs}screen${params.fs}main"
kkonganti@1: include { TOP_UNIQUE_SEROVARS     } from "${params.modules}${params.fs}top_unique_serovars${params.fs}main"
kkonganti@1: include { SOURMASH_SKETCH         } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
kkonganti@1: include { SOURMASH_GATHER         } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
kkonganti@1: include { SOURMASH_SEARCH         } from "${params.modules}${params.fs}sourmash${params.fs}search${params.fs}main"
kkonganti@1: include { KMA_INDEX               } from "${params.modules}${params.fs}kma${params.fs}index${params.fs}main"
kkonganti@1: include { KMA_ALIGN               } from "${params.modules}${params.fs}kma${params.fs}align${params.fs}main"
kkonganti@1: include { OTF_GENOME              } from "${params.modules}${params.fs}otf_genome${params.fs}main"
kkonganti@1: include { SALMON_INDEX            } from "${params.modules}${params.fs}salmon${params.fs}index${params.fs}main"
kkonganti@1: include { SALMON_QUANT            } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
kkonganti@1: include { SOURMASH_COMPARE        } from "${params.modules}${params.fs}custom${params.fs}sourmash${params.fs}compare${params.fs}main"
kkonganti@1: include { BCS_DISTANCE_MATRIX     } from "${params.modules}${params.fs}bcs_distance_matrix${params.fs}main"
kkonganti@1: include { BCS_RESULTS             } from "${params.modules}${params.fs}bcs_results${params.fs}main"
kkonganti@1: include { DUMP_SOFTWARE_VERSIONS  } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@1: include { MULTIQC                 } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL WORKFLOW
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: def reads_platform = 0
kkonganti@1: def salmon_idx_decoys = file ( "${params.salmonidx_decoys}" )
kkonganti@1: 
kkonganti@1: reads_platform += (params.input ? 1 : 0)
kkonganti@1: 
kkonganti@1: if (reads_platform < 1 || reads_platform == 0) {
kkonganti@1:     stopNow("Please mention at least one absolute path to input folder which contains\n" +
kkonganti@1:             "FASTQ files sequenced using the --input option.\n" +
kkonganti@1:         "Ex: --input (Illumina or Generic short reads in FASTQ format)")
kkonganti@1: }
kkonganti@1: 
kkonganti@1: checkMetadataExists(params.mash_sketch, 'MASH sketch')
kkonganti@1: checkMetadataExists(params.tuspy_ps, 'ACC2SERO pickle')
kkonganti@1: checkMetadataExists(params.gsrpy_snp_clus_metadata, 'PDG reference target cluster metadata')
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     RUN THE BETTERCALLSAL WORKFLOW
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: workflow BETTERCALLSAL {
kkonganti@1:     main:
kkonganti@1:         log.info summaryOfParams()
kkonganti@1: 
kkonganti@1:         PROCESS_FASTQ()
kkonganti@1: 
kkonganti@1:         PROCESS_FASTQ
kkonganti@1:             .out
kkonganti@1:             .versions
kkonganti@1:             .set { software_versions }
kkonganti@1: 
kkonganti@1:         PROCESS_FASTQ
kkonganti@1:             .out
kkonganti@1:             .processed_reads
kkonganti@1:             .set { ch_processed_reads }
kkonganti@1: 
kkonganti@1:         if (params.bbmerge_run && !params.fq_single_end) {
kkonganti@1:             ch_processed_reads
kkonganti@1:                 .map { meta, fastq ->
kkonganti@1:                     meta.adapters = (params.bbmerge_adapters ?: params.dummyfile)
kkonganti@1:                     [ meta, fastq ]
kkonganti@1:                 }
kkonganti@1:                 .set { ch_processed_reads }
kkonganti@1:             
kkonganti@1:             BBTOOLS_BBMERGE( ch_processed_reads )
kkonganti@1: 
kkonganti@1:             BBTOOLS_BBMERGE
kkonganti@1:                 .out
kkonganti@1:                 .fastq
kkonganti@1:                 .map { meta, fastq ->
kkonganti@1:                     [ meta, [ fastq ] ]
kkonganti@1:                 }
kkonganti@1:                 .set { ch_processed_reads }
kkonganti@1: 
kkonganti@1:             software_versions
kkonganti@1:                 .mix ( BBTOOLS_BBMERGE.out.versions )
kkonganti@1:                 .set { software_versions }
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         if (params.fastp_run) {
kkonganti@1:             FASTP ( ch_processed_reads )
kkonganti@1: 
kkonganti@1:             FASTP
kkonganti@1:                 .out
kkonganti@1:                 .passed_reads
kkonganti@1:                 .set { ch_processed_reads }
kkonganti@1: 
kkonganti@1:             FASTP
kkonganti@1:                 .out
kkonganti@1:                 .json
kkonganti@1:                 .map { meta, json -> [ json ] }
kkonganti@1:                 .collect()
kkonganti@1:                 .set { ch_multiqc }
kkonganti@1: 
kkonganti@1:             software_versions
kkonganti@1:                 .mix ( FASTP.out.versions )
kkonganti@1:                 .set { software_versions }
kkonganti@1:         } else {
kkonganti@1:             FASTQC ( ch_processed_reads )
kkonganti@1: 
kkonganti@1:             FASTQC
kkonganti@1:                 .out
kkonganti@1:                 .zip
kkonganti@1:                 .map { meta, zip -> [ zip ] }
kkonganti@1:                 .collect()
kkonganti@1:                 .set { ch_multiqc }
kkonganti@1: 
kkonganti@1:             software_versions
kkonganti@1:                 .mix ( FASTQC.out.versions )
kkonganti@1:                 .set { software_versions }
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         if (params.bcs_concat_pe && !params.fq_single_end && !params.bbmerge_run) {
kkonganti@1:             CAT_CAT ( ch_processed_reads )
kkonganti@1: 
kkonganti@1:             CAT_CAT
kkonganti@1:                 .out
kkonganti@1:                 .concatenated_reads
kkonganti@1:                 .set { ch_processed_reads }
kkonganti@1: 
kkonganti@1:             software_versions
kkonganti@1:                 .mix ( CAT_CAT.out.versions )
kkonganti@1:                 .set { software_versions }
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         ch_processed_reads
kkonganti@1:             .map { meta, fastq ->
kkonganti@1:                 meta.sequence_sketch = params.mash_sketch
kkonganti@1:                 meta.get_kma_hit_accs = true
kkonganti@1:                 meta.single_end = true
kkonganti@1:                 meta.salmon_decoys = params.dummyfile
kkonganti@1:                 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
kkonganti@1:                 [ meta, fastq ]
kkonganti@1:             }
kkonganti@1:             .filter { meta, fastq ->
kkonganti@1:                 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
kkonganti@1:                 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toString() ) )
kkonganti@1:                 fq_gzip.read() != -1
kkonganti@1:             }
kkonganti@1:             .set { ch_processed_reads }
kkonganti@1: 
kkonganti@1:         MASH_SCREEN ( ch_processed_reads )
kkonganti@1: 
kkonganti@1:         TOP_UNIQUE_SEROVARS ( MASH_SCREEN.out.screened )
kkonganti@1:         
kkonganti@1:         TOP_UNIQUE_SEROVARS.out.genomes_fasta
kkonganti@1:             .set { ch_genomes_fasta }
kkonganti@1: 
kkonganti@1:         TOP_UNIQUE_SEROVARS.out.failed
kkonganti@1:             .set { ch_bcs_calls_failed }
kkonganti@1: 
kkonganti@1:         if (params.sourmashgather_run || params.sourmashsearch_run) {
kkonganti@1:             SOURMASH_SKETCH (
kkonganti@1:                 ch_processed_reads
kkonganti@1:                     .join ( ch_genomes_fasta )
kkonganti@1:             )
kkonganti@1: 
kkonganti@1:             if (params.sourmashgather_run) {
kkonganti@1:                 SOURMASH_GATHER (
kkonganti@1:                     SOURMASH_SKETCH.out.signatures,
kkonganti@1:                     [], [], [], []
kkonganti@1:                 )
kkonganti@1: 
kkonganti@1:                 SOURMASH_GATHER
kkonganti@1:                     .out
kkonganti@1:                     .genomes_fasta
kkonganti@1:                     .set { ch_genomes_fasta }
kkonganti@1: 
kkonganti@1:                 ch_bcs_calls_failed
kkonganti@1:                     .concat( SOURMASH_GATHER.out.failed )
kkonganti@1:                     .set { ch_bcs_calls_failed }
kkonganti@1: 
kkonganti@1:                 software_versions
kkonganti@1:                     .mix ( SOURMASH_GATHER.out.versions.ifEmpty(null) )
kkonganti@1:                     .set { software_versions }
kkonganti@1:             }
kkonganti@1: 
kkonganti@1:             if (params.sourmashsearch_run) {
kkonganti@1:                 SOURMASH_SEARCH (
kkonganti@1:                     SOURMASH_SKETCH.out.signatures,
kkonganti@1:                     []
kkonganti@1:                 )
kkonganti@1: 
kkonganti@1:                 SOURMASH_SEARCH
kkonganti@1:                     .out
kkonganti@1:                     .genomes_fasta
kkonganti@1:                     .set { ch_genomes_fasta }
kkonganti@1: 
kkonganti@1:                 ch_bcs_calls_failed
kkonganti@1:                     .concat( SOURMASH_SEARCH.out.failed )
kkonganti@1:                     .set { ch_bcs_calls_failed }
kkonganti@1: 
kkonganti@1:                 software_versions
kkonganti@1:                     .mix ( SOURMASH_SEARCH.out.versions.ifEmpty(null) )
kkonganti@1:                     .set { software_versions }
kkonganti@1:             }
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         KMA_INDEX ( ch_genomes_fasta )
kkonganti@1: 
kkonganti@1:         KMA_ALIGN ( 
kkonganti@1:             ch_processed_reads
kkonganti@1:                 .join(KMA_INDEX.out.idx)
kkonganti@1:         )
kkonganti@1: 
kkonganti@1:         OTF_GENOME ( KMA_ALIGN.out.hits )
kkonganti@1: 
kkonganti@1:         OTF_GENOME.out.failed
kkonganti@1:             .concat( ch_bcs_calls_failed )
kkonganti@1:             .collectFile(name: 'BCS_NO_CALLS.txt')
kkonganti@1:             .set { ch_bcs_no_calls }
kkonganti@1: 
kkonganti@1:         SALMON_INDEX ( OTF_GENOME.out.genomes_fasta )
kkonganti@1: 
kkonganti@1:         SALMON_QUANT (
kkonganti@1:             ch_processed_reads
kkonganti@1:                 .join(SALMON_INDEX.out.idx)
kkonganti@1:         )
kkonganti@1: 
kkonganti@1:         SALMON_QUANT
kkonganti@1:             .out
kkonganti@1:             .results
kkonganti@1:             .groupTuple(by: [0])
kkonganti@1:             .map { it -> tuple ( it[1].flatten() ) }
kkonganti@1:             .mix ( ch_bcs_no_calls )
kkonganti@1:             .collect()
kkonganti@1:             .set { ch_salmon_res_dirs }
kkonganti@1: 
kkonganti@1:         if (params.sourmashsketch_run) {
kkonganti@1:             SOURMASH_SKETCH
kkonganti@1:                 .out
kkonganti@1:                 .signatures
kkonganti@1:                 .groupTuple(by: [0])
kkonganti@1:                 .map { meta, qsigs, dsigs ->
kkonganti@1:                     [ qsigs ]
kkonganti@1:                 }
kkonganti@1:                 .collect()
kkonganti@1:                 .flatten()
kkonganti@1:                 .collect()
kkonganti@1:                 .set { ch_query_sigs }
kkonganti@1: 
kkonganti@1:             KMA_ALIGN
kkonganti@1:                 .out
kkonganti@1:                 .hits
kkonganti@1:                 .map { meta, hits ->
kkonganti@1:                     [ hits ]
kkonganti@1:                 }
kkonganti@1:                 .collect()
kkonganti@1:                 .flatten()
kkonganti@1:                 .collectFile(name: 'accessions.txt')
kkonganti@1:                 .set { ch_otf_genomes }
kkonganti@1: 
kkonganti@1:             SOURMASH_COMPARE ( ch_query_sigs, ch_otf_genomes )
kkonganti@1: 
kkonganti@1:             BCS_DISTANCE_MATRIX (
kkonganti@1:                 SOURMASH_COMPARE.out.matrix,
kkonganti@1:                 SOURMASH_COMPARE.out.labels
kkonganti@1:             )
kkonganti@1: 
kkonganti@1:             ch_multiqc
kkonganti@1:                 .concat( BCS_DISTANCE_MATRIX.out.mqc_yml )
kkonganti@1:                 .set { ch_multiqc }
kkonganti@1: 
kkonganti@1:             software_versions
kkonganti@1:                 .mix (
kkonganti@1:                     SOURMASH_SKETCH.out.versions.ifEmpty(null),
kkonganti@1:                     SOURMASH_COMPARE.out.versions.ifEmpty(null),
kkonganti@1:                     BCS_DISTANCE_MATRIX.out.versions.ifEmpty(null),
kkonganti@1:                 )
kkonganti@1:                 .set { software_versions }
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         BCS_RESULTS ( ch_salmon_res_dirs )
kkonganti@1: 
kkonganti@1:         DUMP_SOFTWARE_VERSIONS (
kkonganti@1:             software_versions
kkonganti@1:                 .mix (
kkonganti@1:                     MASH_SCREEN.out.versions,
kkonganti@1:                     TOP_UNIQUE_SEROVARS.out.versions,
kkonganti@1:                     KMA_INDEX.out.versions,
kkonganti@1:                     KMA_ALIGN.out.versions,
kkonganti@1:                     OTF_GENOME.out.versions.ifEmpty(null),
kkonganti@1:                     SALMON_INDEX.out.versions,
kkonganti@1:                     SALMON_QUANT.out.versions,
kkonganti@1:                     BCS_RESULTS.out.versions
kkonganti@1:                 )
kkonganti@1:                 .unique()
kkonganti@1:                 .collectFile(name: 'collected_versions.yml')
kkonganti@1:         )
kkonganti@1: 
kkonganti@1:         DUMP_SOFTWARE_VERSIONS
kkonganti@1:             .out
kkonganti@1:             .mqc_yml
kkonganti@1:             .concat (
kkonganti@1:                 ch_multiqc,
kkonganti@1:                 BCS_RESULTS.out.mqc_yml,
kkonganti@1:                 BCS_RESULTS.out.mqc_json
kkonganti@1:             )
kkonganti@1:             .collect()
kkonganti@1:             .set { ch_multiqc }
kkonganti@1: 
kkonganti@1:         MULTIQC ( ch_multiqc )
kkonganti@1: }
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: workflow.onComplete {
kkonganti@1:     if (workflow.success) {
kkonganti@1:         sendMail()
kkonganti@1:     }
kkonganti@1: }
kkonganti@1: 
kkonganti@1: workflow.onError {
kkonganti@1:     sendMail()
kkonganti@1: }
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     METHOD TO CHECK METADATA EXISTENCE
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: def checkMetadataExists(file_path, msg) {
kkonganti@1:     file_path_obj = file( file_path )
kkonganti@1: 
kkonganti@1:     if (!file_path_obj.exists() || file_path_obj.size() == 0) {
kkonganti@1:         stopNow("Please check if your ${msg} file\n" +
kkonganti@1:             "[ ${file_path} ]\nexists and is not of size 0.")
kkonganti@1:     }
kkonganti@1: }
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: def help() {
kkonganti@1: 
kkonganti@1:     Map helptext = [:]
kkonganti@1:     Map bcsConcatHelp = [:]
kkonganti@1:     Map fastpAdapterHelp = [:]
kkonganti@1: 
kkonganti@1:     bcsConcatHelp['--bcs_concat_pe'] = "Concatenate paired-end files. " +
kkonganti@1:         "Default: ${params.bcs_concat_pe}"
kkonganti@1: 
kkonganti@1:     fastpAdapterHelp['--fastp_use_custom_adapaters'] = "Use custom adapter FASTA with fastp on top of " +
kkonganti@1:         "built-in adapter sequence auto-detection. Enabling this option will attempt to find and remove " +
kkonganti@1:         "all possible Illumina adapter and primer sequences but will make the workflow run slow. " +
kkonganti@1:         "Default: ${params.fastp_use_custom_adapters}"
kkonganti@1: 
kkonganti@1:     helptext.putAll (
kkonganti@1:         fastqEntryPointHelp() +
kkonganti@1:         bcsConcatHelp +
kkonganti@1:         bbmergeHelp(params).text +
kkonganti@1:         fastpHelp(params).text +
kkonganti@1:         fastpAdapterHelp +
kkonganti@1:         mashscreenHelp(params).text +
kkonganti@1:         tuspyHelp(params).text +
kkonganti@1:         sourmashsketchHelp(params).text +
kkonganti@1:         sourmashgatherHelp(params).text +
kkonganti@1:         sourmashsearchHelp(params).text +
kkonganti@1:         sfhpyHelp(params).text +
kkonganti@1:         kmaindexHelp(params).text +
kkonganti@1:         kmaalignHelp(params).text +
kkonganti@1:         salmonidxHelp(params).text +
kkonganti@1:         gsrpyHelp(params).text +
kkonganti@1:         wrapUpHelp()
kkonganti@1:     )
kkonganti@1: 
kkonganti@1:     return addPadding(helptext)
kkonganti@1: }