kkonganti@11: // Define any required imports for this specific workflow
kkonganti@11: import java.nio.file.Paths
kkonganti@11: import nextflow.file.FileHelper
kkonganti@11: 
kkonganti@11: // Include any necessary methods
kkonganti@11: include { \
kkonganti@11:     summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; conciseHelp; \
kkonganti@11:     addPadding; wrapUpHelp   } from "${params.routines}"
kkonganti@11: include { dpubmlstpyHelp     } from "${params.toolshelp}${params.fs}dpubmlstpy"
kkonganti@11: include { fastpHelp          } from "${params.toolshelp}${params.fs}fastp"
kkonganti@11: include { mashscreenHelp     } from "${params.toolshelp}${params.fs}mashscreen"
kkonganti@11: include { tuspyHelp          } from "${params.toolshelp}${params.fs}tuspy"
kkonganti@11: include { spadesHelp         } from "${params.toolshelp}${params.fs}spades"
kkonganti@11: include { shovillHelp        } from "${params.toolshelp}${params.fs}shovill"
kkonganti@11: include { polypolishHelp     } from "${params.toolshelp}${params.fs}polypolish"
kkonganti@11: include { mashtreeHelp       } from "${params.toolshelp}${params.fs}mashtree"
kkonganti@11: include { quastHelp          } from "${params.toolshelp}${params.fs}quast"
kkonganti@11: include { prodigalHelp       } from "${params.toolshelp}${params.fs}prodigal"
kkonganti@11: include { prokkaHelp         } from "${params.toolshelp}${params.fs}prokka"
kkonganti@11: include { pirateHelp         } from "${params.toolshelp}${params.fs}pirate"
kkonganti@11: include { mlstHelp           } from "${params.toolshelp}${params.fs}mlst"
kkonganti@11: include { abricateHelp       } from "${params.toolshelp}${params.fs}abricate"
kkonganti@11: 
kkonganti@11: // Exit if help requested before any subworkflows
kkonganti@11: if (params.help) {
kkonganti@11:     log.info help()
kkonganti@11:     exit 0
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Include any necessary modules and subworkflows
kkonganti@11: include { PROCESS_FASTQ            } from "${params.subworkflows}${params.fs}process_fastq"
kkonganti@11: include { PRODKA                   } from "${params.subworkflows}${params.fs}prodka"
kkonganti@11: include { DOWNLOAD_PUBMLST_SCHEME  } from "${params.modules}${params.fs}download_pubmlst_scheme${params.fs}main"
kkonganti@11: include { DOWNLOAD_REF_GENOME      } from "${params.modules}${params.fs}download_ref_genome${params.fs}main"
kkonganti@11: include { FASTP                    } from "${params.modules}${params.fs}fastp${params.fs}main"
kkonganti@11: include { MASH_SCREEN              } from "${params.modules}${params.fs}mash${params.fs}screen${params.fs}main"
kkonganti@11: include { TOP_UNIQUE_SEROVARS      } from "${params.modules}${params.fs}top_unique_serovars${params.fs}main"
kkonganti@11: include { CAT_UNIQUE               } from "${params.modules}${params.fs}cat${params.fs}unique${params.fs}main"
kkonganti@11: include { SPADES_ASSEMBLE          } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main"
kkonganti@11: include { SHOVILL                  } from "${params.modules}${params.fs}shovill${params.fs}main"
kkonganti@11: include { BWA_IDX_MEM              } from "${params.modules}${params.fs}custom${params.fs}bwa_idx_mem${params.fs}main"
kkonganti@11: include { POLYPOLISH               } from "${params.modules}${params.fs}polypolish${params.fs}main"
kkonganti@11: include { QUAST                    } from "${params.modules}${params.fs}quast${params.fs}main"
kkonganti@11: include { RMLST_POST               } from "${params.modules}${params.fs}rmlst${params.fs}main"
kkonganti@11: include { PIRATE                   } from "${params.modules}${params.fs}pirate${params.fs}main"
kkonganti@11: include { MASHTREE                 } from "${params.modules}${params.fs}mashtree${params.fs}main"
kkonganti@11: include { UPLOAD_MICROREACT        } from "${params.modules}${params.fs}upload_microreact${params.fs}main"
kkonganti@11: include { MLST                     } from "${params.modules}${params.fs}mlst${params.fs}main"
kkonganti@11: include { ABRICATE_RUN             } from "${params.modules}${params.fs}abricate${params.fs}run${params.fs}main"
kkonganti@11: include { ABRICATE_SUMMARY         } from "${params.modules}${params.fs}abricate${params.fs}summary${params.fs}main"
kkonganti@11: include { TABLE_SUMMARY            } from "${params.modules}${params.fs}cat${params.fs}tables${params.fs}main"
kkonganti@11: include { DUMP_SOFTWARE_VERSIONS   } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
kkonganti@11: include { MULTIQC                  } from "${params.modules}${params.fs}multiqc${params.fs}main"
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     INPUTS AND ANY CHECKS FOR THE CRONOLOGY WORKFLOW
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false)
kkonganti@11: def reads_platform = 0
kkonganti@11: def abricate_dbs = [ 'ncbiamrplus', 'resfinder', 'megares', 'argannot' ]
kkonganti@11: 
kkonganti@11: reads_platform += (params.input ? 1 : 0)
kkonganti@11: 
kkonganti@11: if (params.upload_microreact) {
kkonganti@11:     checkMetadataExists(params.microreact_api_key, 'Microreact API Key')
kkonganti@11: }
kkonganti@11: 
kkonganti@11: if (spades_custom_hmm && !spades_custom_hmm.exists()) {
kkonganti@11:     stopNow("Please check if the following SPAdes' custom HMM directory\n" +
kkonganti@11:         "path is valid:\n${params.spades_hmm}\nCannot proceed further!")
kkonganti@11: }
kkonganti@11: 
kkonganti@11: if (reads_platform < 1 || reads_platform == 0) {
kkonganti@11:     stopNow("Please mention at least one absolute path to input folder which contains\n" +
kkonganti@11:             "FASTQ files sequenced using the --input option.\n" +
kkonganti@11:         "Ex: --input (Illumina or Generic short reads in FASTQ format)")
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     RUN THE CRONOLOGY WORKFLOW
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: workflow CRONOLOGY {
kkonganti@11:     main:
kkonganti@11:         ch_mqc_custom_tbl = Channel.empty()
kkonganti@11:         ch_dummy = Channel.fromPath("${params.dummyfile}")
kkonganti@11:         ch_dummy2 = Channel.fromPath("${params.dummyfile2}")
kkonganti@11: 
kkonganti@11:         log.info summaryOfParams()
kkonganti@11: 
kkonganti@11:         PROCESS_FASTQ()
kkonganti@11: 
kkonganti@11:         PROCESS_FASTQ.out.versions
kkonganti@11:             .set { software_versions }
kkonganti@11: 
kkonganti@11:         PROCESS_FASTQ.out.processed_reads
kkonganti@11:             .map { meta, fastq ->
kkonganti@11:                 meta.sequence_sketch = (params.mash_sketch ?: null)
kkonganti@11:                 [meta, fastq]              
kkonganti@11:             }
kkonganti@11:             .set { ch_processed_reads }
kkonganti@11: 
kkonganti@11:         DOWNLOAD_PUBMLST_SCHEME( params.dpubmlstpy_org ?: null )
kkonganti@11: 
kkonganti@11:         DOWNLOAD_REF_GENOME(
kkonganti@11:             (params.ref_acc ? ['id': params.ref_acc] : null)
kkonganti@11:         )
kkonganti@11: 
kkonganti@11:         FASTP( ch_processed_reads )
kkonganti@11: 
kkonganti@11:         FASTP.out.passed_reads
kkonganti@11:             .set { ch_processed_reads }
kkonganti@11: 
kkonganti@11:         FASTP.out.json
kkonganti@11:             .map { meta, json -> [ json ] }
kkonganti@11:             .collect()
kkonganti@11:             .set { ch_multiqc }
kkonganti@11: 
kkonganti@11:         MASH_SCREEN( ch_processed_reads )
kkonganti@11: 
kkonganti@11:         TOP_UNIQUE_SEROVARS( MASH_SCREEN.out.screened )
kkonganti@11: 
kkonganti@11:         TOP_UNIQUE_SEROVARS.out.tsv
kkonganti@11:             .map { meta, tsv -> tsv }
kkonganti@11:             .collectFile(
kkonganti@11:                 name: 'iTOL_metadata_w_dups.txt',
kkonganti@11:                 keepHeader: true,
kkonganti@11:                 skip: 4,
kkonganti@11:                 sort: true
kkonganti@11:             )
kkonganti@11:             .map { file ->
kkonganti@11:                 def meta = [:]
kkonganti@11:                 meta.id = 'Unique iTOL Metadata'
kkonganti@11:                 meta.skip_header = 4
kkonganti@11:                 [meta, file] 
kkonganti@11:             }
kkonganti@11:             .concat(
kkonganti@11:                 TOP_UNIQUE_SEROVARS.out.popup
kkonganti@11:                     .map { meta, popup -> popup }
kkonganti@11:                     .collectFile(
kkonganti@11:                         name: 'iTOL_2_NCBI_Pathogens_w_dups.txt',
kkonganti@11:                         keepHeader: true,
kkonganti@11:                         skip: 3,
kkonganti@11:                         sort: true
kkonganti@11:                     )
kkonganti@11:                     .map { file ->
kkonganti@11:                         def meta = [:]
kkonganti@11:                         meta.id = 'Unique iTOL Popup'
kkonganti@11:                         meta.skip_header = 3
kkonganti@11:                         [meta, file] 
kkonganti@11:                     }
kkonganti@11:             )
kkonganti@11:             .set { ch_uniq }
kkonganti@11: 
kkonganti@11:         TOP_UNIQUE_SEROVARS.out.accessions
kkonganti@11:             .map { meta, acc -> acc }
kkonganti@11:             .splitText()
kkonganti@11:             .collect()
kkonganti@11:             .flatten()
kkonganti@11:             .unique()
kkonganti@11:             .collectFile(name: 'tree_genomes.txt')
kkonganti@11:             .map { genomes -> [ [id: 'hitsTree'], genomes ]}
kkonganti@11:             .set { ch_genomes_fofn }
kkonganti@11: 
kkonganti@11:         CAT_UNIQUE( ch_uniq )
kkonganti@11: 
kkonganti@11:         if (params.fq_single_end) {
kkonganti@11:             SPADES_ASSEMBLE(
kkonganti@11:                 ch_processed_reads
kkonganti@11:                     .combine(ch_dummy)
kkonganti@11:                     .combine(ch_dummy2)
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             SPADES_ASSEMBLE.out.assembly
kkonganti@11:                 .set{ ch_assembly }
kkonganti@11: 
kkonganti@11:             software_versions
kkonganti@11:                 .mix( SPADES_ASSEMBLE.out.versions.ifEmpty(null) )
kkonganti@11:                 .set { software_versions }
kkonganti@11:         } else {
kkonganti@11:             SHOVILL( ch_processed_reads )
kkonganti@11: 
kkonganti@11:             SHOVILL.out.contigs
kkonganti@11:                 .set { ch_assembly }
kkonganti@11: 
kkonganti@11:             software_versions
kkonganti@11:                 .mix( SHOVILL.out.versions.ifEmpty(null) )
kkonganti@11:                 .set { software_versions }
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         if (params.polypolish_run) {
kkonganti@11:             BWA_IDX_MEM(
kkonganti@11:                 ch_assembly
kkonganti@11:                     .join( ch_processed_reads )
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             POLYPOLISH( 
kkonganti@11:                 ch_assembly
kkonganti@11:                     .join( BWA_IDX_MEM.out.aligned_sam )
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             POLYPOLISH.out.polished
kkonganti@11:                 .set { ch_assembly }
kkonganti@11: 
kkonganti@11:             software_versions
kkonganti@11:                 .mix( 
kkonganti@11:                     BWA_IDX_MEM.out.versions,
kkonganti@11:                     POLYPOLISH.out.versions
kkonganti@11:                 )
kkonganti@11:                 .set { software_versions }
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         ch_assembly
kkonganti@11:             .combine( DOWNLOAD_REF_GENOME.out.fasta )
kkonganti@11:             .combine( DOWNLOAD_REF_GENOME.out.gff )
kkonganti@11:             .multiMap { meta, consensus, fasta, gff ->
kkonganti@11:                 sample_fa: consensus
kkonganti@11:                 polished: [meta, consensus]
kkonganti@11:                 ref_fasta: [meta, fasta]
kkonganti@11:                 ref_gff: [meta, gff]
kkonganti@11:             }
kkonganti@11:             .set { ch_quast }
kkonganti@11: 
kkonganti@11:         MASHTREE(
kkonganti@11:             ch_genomes_fofn, 
kkonganti@11:             DOWNLOAD_REF_GENOME.out.fasta
kkonganti@11:                 .concat( ch_quast.sample_fa )
kkonganti@11:                 .collect()
kkonganti@11:         )
kkonganti@11: 
kkonganti@11:         if (params.upload_microreact) {
kkonganti@11:             UPLOAD_MICROREACT(
kkonganti@11:                 MASHTREE.out.nwk
kkonganti@11:                     .map { meta, nwk ->
kkonganti@11:                         nwk
kkonganti@11:                     },
kkonganti@11:                 CAT_UNIQUE.out.csv
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             software_versions
kkonganti@11:                 .mix( 
kkonganti@11:                     UPLOAD_MICROREACT.out.versions
kkonganti@11:                 )
kkonganti@11:                 .set { software_versions }
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         PRODKA( 
kkonganti@11:             ch_quast.ref_fasta,
kkonganti@11:             ch_quast.polished
kkonganti@11:         )
kkonganti@11: 
kkonganti@11:         RMLST_POST( ch_assembly )
kkonganti@11: 
kkonganti@11:         MLST (
kkonganti@11:             ch_assembly
kkonganti@11:                 .combine( DOWNLOAD_PUBMLST_SCHEME.out.pubmlst_dir )
kkonganti@11:         )
kkonganti@11: 
kkonganti@11:         QUAST(
kkonganti@11:             ch_quast.polished,
kkonganti@11:             ch_quast.ref_fasta,
kkonganti@11:             ch_quast.ref_gff
kkonganti@11:         )
kkonganti@11: 
kkonganti@11:         if (params.pirate_run) {
kkonganti@11:             PIRATE(
kkonganti@11:                 PRODKA.out.prokka_gff
kkonganti@11:                     .map { meta, gff ->
kkonganti@11:                         tuple( [id: 'Predicted Genes'], gff )
kkonganti@11:                     }
kkonganti@11:                     .groupTuple(by: [0])
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             software_versions
kkonganti@11:                 .mix( PIRATE.out.versions )
kkonganti@11:                 .set { software_versions }
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         RMLST_POST.out.tsv
kkonganti@11:             .map { meta, tsv -> [ 'rmlst', tsv] }
kkonganti@11:             .groupTuple(by: [0])
kkonganti@11:             .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@11:             .set { ch_mqc_rmlst_tbl }
kkonganti@11: 
kkonganti@11:         MLST.out.tsv
kkonganti@11:             .map { meta, tsv -> [ 'mlst', tsv] }
kkonganti@11:             .groupTuple(by: [0])
kkonganti@11:             .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@11:             .set { ch_mqc_custom_tbl }
kkonganti@11: 
kkonganti@11:         ABRICATE_RUN ( ch_assembly, abricate_dbs )
kkonganti@11: 
kkonganti@11:         ABRICATE_RUN.out.abricated
kkonganti@11:             .map { meta, abres -> [ abricate_dbs, abres ] }
kkonganti@11:             .groupTuple(by: [0])
kkonganti@11:             .map { it -> tuple ( it[0], it[1].flatten() ) }
kkonganti@11:             .set { ch_abricated }
kkonganti@11: 
kkonganti@11:         ABRICATE_SUMMARY ( ch_abricated )
kkonganti@11: 
kkonganti@11:         ch_mqc_custom_tbl
kkonganti@11:             .concat (
kkonganti@11:                 ch_mqc_rmlst_tbl,
kkonganti@11:                 ABRICATE_SUMMARY.out.ncbiamrplus.map { it -> tuple ( it[0], it[1] )},
kkonganti@11:                 ABRICATE_SUMMARY.out.resfinder.map { it -> tuple ( it[0], it[1] )},
kkonganti@11:                 ABRICATE_SUMMARY.out.megares.map { it -> tuple ( it[0], it[1] )},
kkonganti@11:                 ABRICATE_SUMMARY.out.argannot.map { it -> tuple ( it[0], it[1] )},
kkonganti@11:             )
kkonganti@11:             .groupTuple(by: [0])
kkonganti@11:             .map { it -> [ it[0], it[1].flatten() ]}
kkonganti@11:             .set { ch_mqc_custom_tbl }
kkonganti@11: 
kkonganti@11:         TABLE_SUMMARY ( ch_mqc_custom_tbl )
kkonganti@11: 
kkonganti@11:         DUMP_SOFTWARE_VERSIONS (
kkonganti@11:             software_versions
kkonganti@11:             .mix(
kkonganti@11:                     DOWNLOAD_PUBMLST_SCHEME.out.versions,
kkonganti@11:                     DOWNLOAD_REF_GENOME.out.versions,
kkonganti@11:                     FASTP.out.versions,
kkonganti@11:                     MASH_SCREEN.out.versions,
kkonganti@11:                     TOP_UNIQUE_SEROVARS.out.versions,
kkonganti@11:                     CAT_UNIQUE.out.versions,
kkonganti@11:                     MASHTREE.out.versions,
kkonganti@11:                     POLYPOLISH.out.versions,
kkonganti@11:                     QUAST.out.versions,
kkonganti@11:                     PRODKA.out.versions,
kkonganti@11:                     RMLST_POST.out.versions,
kkonganti@11:                     MLST.out.versions,
kkonganti@11:                     ABRICATE_RUN.out.versions,
kkonganti@11:                     ABRICATE_SUMMARY.out.versions,
kkonganti@11:                     TABLE_SUMMARY.out.versions
kkonganti@11:                 )
kkonganti@11:                 .unique()
kkonganti@11:                 .collectFile(name: 'collected_versions.yml')
kkonganti@11:         )
kkonganti@11: 
kkonganti@11:         DUMP_SOFTWARE_VERSIONS.out.mqc_yml
kkonganti@11:             .concat (
kkonganti@11:                 ch_multiqc,
kkonganti@11:                 TABLE_SUMMARY.out.mqc_yml,
kkonganti@11:                 PRODKA.out.prokka_txt.map { meta, txt -> txt },
kkonganti@11:                 QUAST.out.results.map { meta, res -> res }
kkonganti@11:             )
kkonganti@11:             .collect()
kkonganti@11:             .set { ch_multiqc }
kkonganti@11: 
kkonganti@11:         MULTIQC( ch_multiqc )
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: workflow.onComplete {
kkonganti@11:     if (workflow.success) {
kkonganti@11:         sendMail()
kkonganti@11:     }
kkonganti@11: }
kkonganti@11: 
kkonganti@11: workflow.onError {
kkonganti@11:     sendMail()
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     METHOD TO CHECK FILE EXISTENCE
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: def checkMetadataExists(file_path, msg) {
kkonganti@11:     file_path_obj = file( file_path )
kkonganti@11:     
kkonganti@11:     if (msg.toString().find(/(?i)KMA/)) {
kkonganti@11:         if (!file_path_obj.parent.exists() || file_path_obj.parent.size() == 0) {
kkonganti@11:             stopNow("Please check if your ${msg}\n" +
kkonganti@11:                 "[ ${file_path} ]\nexists and that the files are not of size 0.")
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11:     else if (!file_path_obj.exists() || file_path_obj.size() == 0) {
kkonganti@11:         stopNow("Please check if your ${msg} file\n" +
kkonganti@11:             "[ ${file_path} ]\nexists and is not of size 0.")
kkonganti@11:     }
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     HELP TEXT METHODS FOR CRONOLOGY WORKFLOW
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: def help() {
kkonganti@11: 
kkonganti@11:     Map helptext = [:]
kkonganti@11:     Map nH = [:]
kkonganti@11:     Map fastpAdapterHelp = [:]
kkonganti@11:     def uHelp = (params.help.getClass().toString() =~ /String/ ? params.help.tokenize(',').join(' ') : '')
kkonganti@11: 
kkonganti@11:     Map defaultHelp = [
kkonganti@11:         '--help dpubmlstpy' : 'Show dl_pubmlst_profiles_and_schemes.py CLI options',
kkonganti@11:         '--help fastp'      : 'Show fastp CLI options',
kkonganti@11:         '--help spades'     : 'Show spades CLI options',
kkonganti@11:         '--help shovill'    : 'Show shovill CLI options',
kkonganti@11:         '--help polypolish' : 'Show polypolish CLI options',
kkonganti@11:         '--help quast'      : 'Show quast.py CLI options',
kkonganti@11:         '--help prodigal'   : 'Show prodigal CLI options',
kkonganti@11:         '--help prokka'     : 'Show prokka CLI options',
kkonganti@11:         '--help pirate'     : 'Show priate CLI options',
kkonganti@11:         '--help mlst'       : 'Show mlst CLI options',
kkonganti@11:         '--help mash'       : 'Show mash `screen` CLI options',
kkonganti@11:         '--help tree'       : 'Show mashtree CLI options',
kkonganti@11:         '--help abricate'   : 'Show abricate CLI options\n'
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     fastpAdapterHelp['--fastp_use_custom_adapaters'] = "Use custom adapter FASTA with fastp on top of " +
kkonganti@11:         "built-in adapter sequence auto-detection. Enabling this option will attempt to find and remove " +
kkonganti@11:         "all possible Illumina adapter and primer sequences but will make the workflow run slow. " +
kkonganti@11:         "Default: ${params.fastp_use_custom_adapters}"
kkonganti@11: 
kkonganti@11:     if (params.help.getClass().toString() =~ /Boolean/ || uHelp.size() == 0) {
kkonganti@11:         println conciseHelp('fastp,polypolish')
kkonganti@11:         helptext.putAll(defaultHelp)
kkonganti@11:     } else {
kkonganti@11:         params.help.tokenize(',').each { h ->
kkonganti@11:             if (defaultHelp.keySet().findAll{ it =~ /(?i)\b${h}\b/ }.size() == 0) {
kkonganti@11:                 println conciseHelp('fastp,polypolish')
kkonganti@11:                 stopNow("Tool [ ${h} ] is not a part of ${params.pipeline} pipeline.")
kkonganti@11:             }
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         helptext.putAll(
kkonganti@11:             fastqEntryPointHelp() +
kkonganti@11:             (uHelp =~ /(?i)\bdpubmlstpy/ ? dpubmlstpyHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bfastp/ ? fastpHelp(params).text + fastpAdapterHelp : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bmash/ ? mashscreenHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\btuspy/ ? tuspyHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bspades/ ? spadesHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bshovill/ ? shovillHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bpolypolish/ ? polypolishHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bquast/ ? quastHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bprodigal/ ? prodigalHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bprokka/ ? prokkaHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bpirate/ ? pirateHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\bmlst/ ? mlstHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\btree/ ? mashtreeHelp(params).text : nH) +
kkonganti@11:             (uHelp =~ /(?i)\babricate/ ? abricateHelp(params).text : nH) +
kkonganti@11:             wrapUpHelp()
kkonganti@11:         )
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return addPadding(helptext)
kkonganti@11: }