add contig anno

Author: rujinlong

main.nf

@@ -24,6 +24,7 @@ WorkflowMain.initialise(workflow, params, log)
 */
 
 include { VIROPROFILER } from './workflows/viroprofiler'
+include { CONTIGANNO } from './workflows/contig_anno'
 
 
 /*
@@ -36,7 +37,11 @@ include { VIROPROFILER } from './workflows/viroprofiler'
 // WORKFLOW: Run main deng-lab/viroprofiler analysis pipeline
 //
 workflow {
-    VIROPROFILER ()
+    if (params.input_contigs) {
+        CONTIGANNO()
+    } else {
+        VIROPROFILER ()
+    }
 }
 
 /*

workflows/contig_anno.nf

@@ -0,0 +1,164 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    VALIDATE INPUTS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+// Validate input parameters
+WorkflowViroprofiler.initialise(params, log)
+
+// TODO nf-core: Add all file path parameters for the pipeline to the list below
+// Check input path parameters to see if they exist
+def checkPathParamList = [ params.multiqc_config ]
+for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
+
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    CONFIG FILES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT LOCAL MODULES/SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
+//
+include { INPUT_CHECK             } from '../subworkflows/local/input_check'
+include { vMAG_PHAMB; vMAG_VRHYME } from '../subworkflows/local/vMAG'
+include { SETUP } from '../subworkflows/local/init'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT NF-CORE MODULES/SUBWORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// MODULE: Installed directly from nf-core/modules
+//
+
+
+include { FASTQC                       } from '../modules/nf-core/modules/fastqc/main'
+include { MULTIQC                      } from '../modules/nf-core/modules/multiqc/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS  } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
+include { FASTP                        } from '../modules/nf-core/modules/fastp/main'
+include { SPADES                       } from '../modules/nf-core/modules/spades/main'
+include { BBMAP_ALIGN                  } from '../modules/nf-core/modules/bbmap/align/main'
+// local modules
+include { DECONTAM                     } from '../modules/local/decontam'
+include { CONTIGLIB; CONTIGLIB_CLUSTER } from '../modules/local/contig_library'
+include { MAPPING2CONTIGS; CONTIGINDEX; MAPPING2CONTIGS2; ABUNDANCE   } from '../modules/local/abundance'
+include { BRACKEN_DB; BRACKEN; BRACKEN_COMBINEBRACKENOUTPUTS } from '../modules/local/bracken'
+include { DRAMV; EMAPPER; ABRICATE     } from '../modules/local/annotation'
+include { VIRALHOST_IPHOP              } from '../modules/local/viral_host'
+include { BACPHLIP; REPLIDEC           } from '../modules/local/replicyc'
+include { CHECKV; VIRSORTER2; DVF; VIRCONTIGS_PRE; VIBRANT           } from '../modules/local/viral_detection'
+include { GENEPRED as GENEPRED4CTG; NRSEQS as NRPROT; NRSEQS as NRGENE } from '../modules/local/gene_library'
+include { TAXONOMY_VCONTACT; TAXONOMY_MMSEQS; TAXONOMY_MERGE           } from '../modules/local/taxonomy'
+include { RESULTS_TSE                  } from '../modules/local/base'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN MAIN WORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+// Info required for completion email and summary
+def multiqc_report = []
+
+workflow CONTIGANNO {
+    ch_cclib = Channel.fromPath("${params.input_contigs}", checkIfExists: true).first()
+    // MODULE: CheckV
+    CHECKV(ch_cclib)
+    clean_cclib_long = CHECKV.out.checkv_qc_ch
+    ch_nrclib = clean_cclib_long
+
+    // Gene library
+    GENEPRED4CTG (clean_cclib_long, "ccclib_long")
+    ch_prot_all = GENEPRED4CTG.out.prot_ch
+    ch_gene_all = GENEPRED4CTG.out.gene_fna_ch
+
+    // Non-redundant gene library
+    NRPROT (ch_prot_all, "prot", params.prot_cluster_min_similarity, params.prot_cluster_min_coverage)
+    ch_nr_prot = NRPROT.out.cluster_rep_ch
+    NRGENE (ch_gene_all, "gene", params.gene_cluster_min_similarity, params.gene_cluster_min_coverage)
+    ch_nr_gene = NRGENE.out.cluster_rep_ch
+
+    // Gene/Protein annotation
+    if (params.use_eggnog) {
+        EMAPPER (ch_nr_prot)
+    }
+    if (params.use_abricate) {
+        ABRICATE (ch_nr_gene)
+    }
+
+
+    // Viral detection: DVF + CheckV MQ, HQ, Complete + VirSorter2 + VIBRANT
+    VIBRANT(ch_nrclib)
+    DVF(ch_nrclib)
+    ch_dvfscore = DVF.out.dvfscore_ch
+    ch_dvfseq = DVF.out.dvfseq_ch
+    ch_dvflist = DVF.out.dvflist_ch
+
+    VIRCONTIGS_PRE(ch_nrclib, ch_dvflist, CHECKV.out.checkv2vContigs_ch, VIBRANT.out.vibrant_ch)
+    ch_putative_vList =  VIRCONTIGS_PRE.out.putative_vList_ch
+    ch_putative_vContigs =  VIRCONTIGS_PRE.out.putative_vContigs_ch
+    vContigs_and_vMAGs = ch_putative_vContigs
+
+    VIRSORTER2(ch_nrclib)        // for DRAM-v gene annotation and AMG detection
+    ch_vs2contigs = VIRSORTER2.out.vs2_contigs_ch
+
+    // ANNOTATION (AMG)
+    if ( params.use_dram ) {
+        DRAMV (ch_vs2contigs, VIRSORTER2.out.vs2_affi_ch)
+    }
+
+    // Taxonomy
+    TAXONOMY_VCONTACT(ch_nrclib)
+    TAXONOMY_MMSEQS(ch_nrclib)
+    TAXONOMY_MERGE(TAXONOMY_VCONTACT.out.taxa_vc_ch, TAXONOMY_MMSEQS.out.taxa_mmseqs_ch)
+
+    // Viral host
+    if ( params.use_iphop ) {
+        VIRALHOST_IPHOP(ch_nrclib)
+    }
+
+    // Replication cycle
+    BACPHLIP (ch_nrclib)
+    ch_replicyc = BACPHLIP.out.bacphlip_ch
+
+    //
+    // MODULE: MultiQC
+    //
+    workflow_summary    = WorkflowViroprofiler.paramsSummaryMultiqc(workflow, summary_params)
+    ch_workflow_summary = Channel.value(workflow_summary)
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    COMPLETION EMAIL AND SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow.onComplete {
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    }
+    NfcoreTemplate.summary(workflow, params, log)
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    THE END
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/