Iqtree version bump and output fix

modules/nf-core/iqtree/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::iqtree=2.3.0
+  - bioconda::iqtree=2.3.4

modules/nf-core/iqtree/main.nf

@@ -4,34 +4,87 @@ process IQTREE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/iqtree:2.3.0--h21ec9f0_0' :
-        'biocontainers/iqtree:2.3.0--h21ec9f0_0' }"
+        'https://depot.galaxyproject.org/singularity/iqtree:2.3.4--h21ec9f0_0' :
+        'biocontainers/iqtree:2.3.4--h21ec9f0_0' }"
 
     input:
-    tuple val(meta), path(alignment)
-    val constant_sites
+    tuple val(meta), path(alignment), path(tree)
+    path(tree_te)
+    path(lmclust)
+    path(mdef)
+    path(partitions_equal)
+    path(partitions_proportional)
+    path(partitions_unlinked)
+    path(guide_tree)
+    path(sitefreq_in)
+    path(constraint_tree)
+    path(trees_z)
+    path(suptree)
+    path(trees_rf)
 
     output:
-    tuple val(meta), path("*.treefile") , emit: phylogeny
-    tuple val(meta), path("*.iqtree")   , emit: report
-    tuple val(meta), path("*.mldist")   , emit: mldist, optional: true
-    tuple val(meta), path("*.ufboot")   , emit: bootstrap, optional: true
-    tuple val(meta), path("*.log")      , emit: log
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*.treefile")      , emit: phylogeny     , optional: true
+    tuple val(meta), path("*.iqtree")        , emit: report        , optional: true
+    tuple val(meta), path("*.mldist")        , emit: mldist        , optional: true
+    tuple val(meta), path("*.lmap.svg")      , emit: lmap_svg      , optional: true
+    tuple val(meta), path("*.lmap.eps")      , emit: lmap_eps      , optional: true
+    tuple val(meta), path("*.lmap.quartetlh"), emit: lmap_quartetlh, optional: true
+    tuple val(meta), path("*.sitefreq")      , emit: sitefreq_out  , optional: true
+    tuple val(meta), path("*.ufboot")        , emit: bootstrap     , optional: true
+    tuple val(meta), path("*.state")         , emit: state         , optional: true
+    tuple val(meta), path("*.contree")       , emit: contree       , optional: true
+    tuple val(meta), path("*.nex")           , emit: nex           , optional: true
+    tuple val(meta), path("*.splits")        , emit: splits        , optional: true
+    tuple val(meta), path("*.suptree")       , emit: suptree       , optional: true
+    tuple val(meta), path("*.alninfo")       , emit: alninfo       , optional: true
+    tuple val(meta), path("*.partlh")        , emit: partlh        , optional: true
+    tuple val(meta), path("*.siteprob")      , emit: siteprob      , optional: true
+    tuple val(meta), path("*.sitelh")        , emit: sitelh        , optional: true
+    tuple val(meta), path("*.treels")        , emit: treels        , optional: true
+    tuple val(meta), path("*.rate  ")        , emit: rate          , optional: true
+    tuple val(meta), path("*.mlrate")        , emit: mlrate        , optional: true
+    tuple val(meta), path("GTRPMIX.nex")     , emit: exch_matrix   , optional: true
+    tuple val(meta), path("*.log")           , emit: log
+    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(' ', '')
-    def prefix      = task.ext.prefix ?: meta.id
+    def args                        = task.ext.args           ?: ''
+    def alignment_arg               = alignment               ? "-s $alignment"                 : ''
+    def tree_arg                    = tree                    ? "-t $tree"                      : ''
+    def tree_te_arg                 = tree_te                 ? "-te $tree_te"                  : ''
+    def lmclust_arg                 = lmclust                 ? "-lmclust $lmclust"             : ''
+    def mdef_arg                    = mdef                    ? "-mdef $mdef"                   : ''
+    def partitions_equal_arg        = partitions_equal        ? "-q $partitions_equal"          : ''
+    def partitions_proportional_arg = partitions_proportional ? "-spp $partitions_proportional" : ''
+    def partitions_unlinked_arg     = partitions_unlinked     ? "-sp $partitions_unlinked"      : ''
+    def guide_tree_arg              = guide_tree              ? "-ft $guide_tree"               : ''
+    def sitefreq_in_arg             = sitefreq_in             ? "-fs $sitefreq_in"              : ''
+    def constraint_tree_arg         = constraint_tree         ? "-g $constraint_tree"           : ''
+    def trees_z_arg                 = trees_z                 ? "-z $trees_z"                   : ''
+    def suptree_arg                 = suptree                 ? "-sup $suptree"                 : ''
+    def trees_rf_arg                = trees_rf                ? "-rf $trees_rf"                 : ''
+    def prefix                      = task.ext.prefix         ?: meta.id
+    def memory                      = task.memory.toString().replaceAll(' ', '')
     """
     iqtree \\
-        $fconst_args \\
         $args \\
-        -s $alignment \\
+        $alignment_arg \\
+        $tree_arg \\
+        $tree_te_arg \\
+        $lmclust_arg \\
+        $mdef_arg \\
+        $partitions_equal_arg \\
+        $partitions_proportional_arg \\
+        $partitions_unlinked_arg \\
+        $guide_tree_arg \\
+        $sitefreq_in_arg \\
+        $constraint_tree_arg \\
+        $trees_z_arg \\
+        $suptree_arg \\
+        $trees_rf\\
         -pre $prefix \\
         -nt AUTO \\
         -ntmax $task.cpus \\
@@ -46,11 +99,28 @@ process IQTREE {
     stub:
     def prefix = task.ext.prefix ?: meta.id
     """
-    touch ${prefix}.treefile
-    touch ${prefix}.iqtree
-    touch ${prefix}.mldist
-    touch ${prefix}.ufboot
-    touch ${prefix}.log
+    touch "${prefix}.treefile"
+    touch "${prefix}.iqtree"
+    touch "${prefix}.mldist"
+    touch "${prefix}.lmap.svg"
+    touch "${prefix}.lmap.eps"
+    touch "${prefix}.lmap.quartetlh"
+    touch "${prefix}.sitefreq"
+    touch "${prefix}.ufboot"
+    touch "${prefix}.state"
+    touch "${prefix}.contree"
+    touch "${prefix}.nex"
+    touch "${prefix}.splits"
+    touch "${prefix}.suptree"
+    touch "${prefix}.alninfo"
+    touch "${prefix}.partlh"
+    touch "${prefix}.siteprob"
+    touch "${prefix}.sitelh"
+    touch "${prefix}.treels"
+    touch "${prefix}.rate"
+    touch "${prefix}.mlrate"
+    touch "GTRPMIX.nex"
+    touch "${prefix}.log"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/iqtree/meta.yml

@@ -16,47 +16,201 @@ input:
   - meta:
       type: map
       description: |
-        Groovy map containing sample information
-        e.g. [ id: 'test' ]
+        Groovy map containing sample information for the
+        alignment/tree file, e.g. [ id: 'test' ]
   - alignment:
       type: file
-      description: A FASTA format multiple sequence alignment file
-      pattern: "*.{fasta,fas,fa,mfa}"
-  - constant_sites:
-      type: string
-      description: Number of constant sites to add,
-        see iqtree documentation for details
-        (http://www.iqtree.org/doc/Command-Reference)
-output:
-  - versions:
+      description: Input alignment file in PHYLIP,
+        FASTA, NEXUS, CLUSTAL or MSF format (-s)
+      pattern: "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}"
+  - tree:
       type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      description: "File containing one or multiple phylogenetic trees (-t):
+        - Single tree used e.g. as starting tree for tree search
+        - Set of trees used e.g. for distance computation, consensus tree construction"
+      pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}"
+  - tree_te:
+      type: file
+      description: "File containing single phylogenetic tree (-te)
+        Use cases:
+        - fixed user tree to skip tree search
+        - ancestral sequence reconstruction"
+      pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}"
+  - lmclust:
+      type: file
+      description: NEXUS file containing taxon clusters
+        for quartet mapping analysis (-lmclust)
+      pattern: "*.nex{us}"
+  - mdef:
+      type: file
+      description: NEXUS model file defining new models (-mdef)
+      pattern: "*.nex{us}"
+  - partitions_equal:
+      type: file
+      description: Partition file for edge-equal partition
+        model, all partitions share same set of branch lengths (-q)
+      pattern: "*.{nex,nexus,tre,tree,treefile}"
+  - partitions_proportional:
+      type: file
+      description: Partition file for edge-equal partition
+        model, all partitions share same set of branch lengths (-spp)
+      pattern: "*.{nex,nexus,tre,tree,treefile}"
+  - partitions_unlinked:
+      type: file
+      description: Partition file for edge-equal partition
+        model, all partitions share same set of branch lengths (-sp)
+      pattern: "*.{nex,nexus,tre,tree,treefile}"
+  - guide_tree:
+      type: file
+      description: File containing guide tree for inference of
+        site frequency profiles (-ft)
+      pattern: "*.{nex,nexus,tre,tree,treefile}"
+  - sitefreq_in:
+      type: file
+      description: Site frequency file (-fs)
+      pattern: "*.sitefreq"
+  - constraint_tree:
+      type: file
+      description: File containing opological constraint tree in
+        NEWICK format. The constraint tree can be a multifurcating
+        tree and need not to include all taxa. (-g)
+      pattern: "*.{nwk,newick}"
+  - trees_z:
+      type: file
+      description: File containing a set of trees for which
+        log-likelihoods should be computed (-z)
+  - suptree:
+      type: file
+      description: File containing input “target” tree, support
+        values are extracted from trees passed via -t, and mapped
+        onto the target tree (-sup)
+  - trees_rf:
+      type: file
+      description: "File containing a second tree set (-rf). Used
+        for computing the distance to the primary tree set (`tree`)"
+      pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}"
+output:
   - phylogeny:
       type: file
       description: A phylogeny in Newick format
       pattern: "*.{treefile}"
-  - bootstrap:
-      type: file
-      description: |
-        A file containing all bootstrap trees,
-        only generated if bootstrap is on
-        and the -wbt flag is passed in ext.args
-      pattern: "*.{ufboot}"
   - report:
       type: file
       description: |
         Main report file containing computational
-        results as well as a textual visualisation
-        of the final tree.
+        results as well as a textual visualization
+        of the final tree
+      pattern: "*.{iqtree}"
   - mldist:
       type: file
       description: |
         File containing the pairwise maximum
-        likelihood distances as a matrix.
+        likelihood distances as a matrix
+      pattern: "*.{mldist}"
+  - lmap_svg:
+      type: file
+      description: |
+        File containing likelihood mapping analysis
+        results in .svg format (-lmap/-lmclust)
+      pattern: "*.lmap.svg"
+  - lmap_eps:
+      type: file
+      description: |
+        File containing likelihood mapping analysis
+        results in .eps format (-lmap/-lmclust)
+      pattern: "*.lmap.eps"
+  - lmap_quartetlh:
+      type: file
+      description: |
+        File containing quartet log-likelihoods (-wql)
+      pattern: "*.lmap.quartetlh"
+  - sitefreq_out:
+      type: file
+      description: |
+        File containing site frequency profiles (-ft)
+      pattern: "*.sitefreq"
+  - bootstrap:
+      type: file
+      description: |
+        File containing all bootstrap trees (-wbt/-wbtl)
+      pattern: "*.ufboot"
+  - state:
+      type: file
+      description: |
+        File containing ancestral sequences for all
+        nodes of the tree by empirical Bayesian method (-asr)
+      pattern: "*.{state}"
+  - contree:
+      type: file
+      description: |
+        File containing consensus tree (-con/-bb)
+      pattern: "*.{contree}"
+  - nex:
+      type: file
+      description: |
+        File containing consensus network (-net/-bb)
+      pattern: "*.{nex}"
+  - splits:
+      type: file
+      description: |
+        File containing consensus network in star-dot format (-wsplits)
+      pattern: "*.{splits}"
+  - suptree:
+      type: file
+      description: |
+        File containing tree with assigned support
+        values based on supplied "target" tree (-sup)
+      pattern: "*.{suptree}"
+  - alninfo:
+      type: file
+      description: |
+        File containing alignment site statistics (-alninfo)
+      pattern: "*.{alninfo}"
+  - partlh:
+      type: file
+      description: |
+        File containing partition log-likelihoods (-wpl)
+      pattern: "*.{partlh}"
+  - siteprob:
+      type: file
+      description: |
+        File containing site posterior probabilities (-wspr/-wspm/-wspmr)
+      pattern: "*.{siteprob}"
+  - sitelh:
+      type: file
+      description: |
+        File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr)
+      pattern: "*.{sitelh}"
+  - treels:
+      type: file
+      description: |
+        File containing all locally optimal trees (-wt)
+      pattern: "*.{treels}"
+  - rate:
+      type: file
+      description: |
+        File containing inferred site-specific
+        evolutionary rates (-wsr)
+      pattern: "*.{rate}"
+  - mlrate:
+      type: file
+      description: |
+        File containing site-specific subtitution
+        rates determined by maximum likelihood (--mlrate)
+      pattern: "*.{mlrate}"
+  - exch_matrix:
+      type: file
+      description: File containing the exchangeability
+        matrix obtained from the optimization (--link-exchange-rates)
+      pattern: "GTRPMIX.nex"
   - log:
       type: file
       description: Log file of entire run
+      pattern: "*.{log}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
   - "@avantonder"
   - "@aunderwo"

modules/nf-core/iqtree/tests/iqtree_bootstrap.config

@@ -0,0 +1,5 @@
+process {
+    withName: "IQTREE" {
+        ext.args = "-bb 1000 -wbt -wsplits -m LG"
+    }
+}

modules/nf-core/iqtree/tests/iqtree_optional.config

@@ -0,0 +1,5 @@
+process {
+    withName: "IQTREE" {
+        ext.args = "-m C10 -asr -alninfo -wpl -wspr -wsl -wsr --mlrate -lmap 150 -wql --mlrate"
+    }
+}

modules/nf-core/iqtree/tests/bootstrap.config → modules/nf-core/iqtree/tests/iqtree_treels.config

@@ -1,5 +1,5 @@
 process {
     withName: "IQTREE" {
-        ext.args = "-bb 1000 -wbt"
+        ext.args = "-m LG -wt"
     }
 }