added IQtree and core to rename fasta headers for use with IQtree

conf/modules.config

@@ -90,4 +90,12 @@ process {
     withName: BAKTA_BAKTA {
         ext.args = '--force'
     }
+
+    withName: MAFFT {
+        ext.prefix = { "${fasta.getSimpleName()}_aligned" }
+    }
+
+    withName: IQTREE2 {
+        ext.args = '-B 1000'
+    }
 }

modules.json

@@ -50,6 +50,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "iqtree": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
                     "mafft": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

modules/local/iqtree2.nf

@@ -0,0 +1,39 @@
+process IQTREE2 {
+    tag "$alignment"
+    label 'process_medium'
+
+    conda "bioconda::iqtree=2.1.4_beta"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' :
+        'biocontainers/iqtree:2.1.4_beta--hdcc8f71_0' }"
+
+    input:
+    tuple val(meta), path(alignment)
+    val constant_sites
+
+    output:
+    tuple val(meta), path("*.treefile"), emit: phylogeny
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
+    def memory      = task.memory.toString().replaceAll(' ', '')
+    """
+    iqtree2 \\
+        $fconst_args \\
+        $args \\
+        -s $alignment \\
+        -nt AUTO \\
+        -ntmax $task.cpus \\
+        -mem $memory \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        iqtree: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
+    END_VERSIONS
+    """
+}

modules/local/rename_core_gene_headers.nf

@@ -0,0 +1,31 @@
+process RENAMECOREGENEHEADERS {
+    tag "$ref_meta.id"
+    label 'process_single'
+
+    conda "conda-forge::coreutils=9.1"                                          
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :            
+        'ubuntu:20.04' }"                                                       
+
+    input:
+    tuple val(ref_meta), path(feat_seqs)
+
+    output:
+    tuple val(ref_meta), path("${prefix}_feat_seqs_renamed"), emit: feat_seqs
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    prefix = task.ext.prefix ?: "${ref_meta.id}"
+    """
+    # Create folder for output
+    mkdir ${prefix}_feat_seqs_renamed
+
+    # Rename headers to just sample ID
+    for file in ${feat_seqs}/*.fasta
+    do
+        sed 's/>.*genome:\\(.*\\)gene.*/>\\1/g' \$file > ${prefix}_feat_seqs_renamed/\$(basename \$file)
+    done
+    """
+}

subworkflows/local/core_genome_phylogeny.nf

@@ -1,9 +1,11 @@
 include { PIRATE                } from '../../modules/nf-core/pirate/main'
 include { SAMTOOLS_FAIDX        } from '../../modules/nf-core/samtools/faidx/main'
 include { MAFFT                 } from '../../modules/nf-core/mafft/main'
+include { IQTREE2               } from '../../modules/local/iqtree2'
 include { REFORMATPIRATERESULTS } from '../../modules/local/reformat_pirate_results'
 include { ALIGNFEATURESEQUENCES } from '../../modules/local/align_feature_sequences'
 include { SUBSETCOREGENES       } from '../../modules/local/subset_core_genes'
+include { RENAMECOREGENEHEADERS } from '../../modules/local/rename_core_gene_headers'
 
 workflow CORE_GENOME_PHYLOGENY {
 
@@ -28,12 +30,20 @@ workflow CORE_GENOME_PHYLOGENY {
     // Extract sequences of all genes (does not align, contrary to current name)
     ALIGNFEATURESEQUENCES ( PIRATE.out.results )                            
     ch_versions = ch_versions.mix(ALIGNFEATURESEQUENCES.out.versions.first())
+
+    // Rename FASTA file headers to start with just sample ID for use with IQTREE
+    RENAMECOREGENEHEADERS ( ALIGNFEATURESEQUENCES.out.feat_seqs )
 
-    // Filter for core single copy genes and link their extracted sequences to a new folder
-    SUBSETCOREGENES ( REFORMATPIRATERESULTS.out.gene_fam.join(ALIGNFEATURESEQUENCES.out.feat_seqs) )
+    // Filter for core single copy genes with no paralogs
+    SUBSETCOREGENES ( REFORMATPIRATERESULTS.out.gene_fam.join(RENAMECOREGENEHEADERS.out.feat_seqs) )
 
     // Align each gene family with mafft
-    MAFFT( SUBSETCOREGENES.out.feat_seq.transpose(), [] )                                         
+    MAFFT ( SUBSETCOREGENES.out.feat_seq.transpose(), [] )
+    ch_versions = ch_versions.mix(MAFFT.out.versions.first())
+
+    // Inferr phylogenetic tree from aligned core genes
+    IQTREE2 ( MAFFT.out.fas.groupTuple(), [] )
+    ch_versions = ch_versions.mix(IQTREE2.out.versions.first())                           
 
     emit:
     pirate_aln      = PIRATE.out.aln        // channel: [ ref_meta, align_fasta ]