Merge pull request #2 from artic-network/dev

Add squirrel v1.0.8 options

main.nf

@@ -6,7 +6,8 @@ process squirrel {
 
   input:
     path fasta
-    path refs
+    path "refs.fa"
+    path "bg.fa"
     path additional_mask
 
   output:
@@ -20,7 +21,7 @@ process squirrel {
     if ( params.seq_qc )
         extra += " --seq-qc"
     if ( params.assembly_refs )
-        extra += " --assembly-refs ${refs}"
+        extra += " --assembly-refs refs.fa"
     if ( params.no_mask )
         extra += " --no-mask"
     if ( params.no_itr_mask )
@@ -35,8 +36,12 @@ process squirrel {
         extra += " --clade ${params.clade}"
     if ( params.run_phylo )
         extra += " --run-phylo"
+    if ( params.run_abobec3_phylo )
+        extra += " --run-apobec3-phylo"
     if ( params.include_background )
         extra += " --include-background"
+    if ( params.additional_background )
+        extra += " -bf bg.fa"
     if ( params.outgroups )
         extra += " --outgroups ${params.outgroups}"
 
@@ -52,13 +57,19 @@ workflow {
       refs_ch = channel.fromPath("${projectDir}/${params.default_assembly_refs}", checkIfExists:true)
   }
 
-if ( params.additional_mask ) {
+  if ( params.additional_background ) {
+      bg_ch = channel.fromPath("${params.additional_background}", checkIfExists:true)
+  } else {
+      bg_ch = channel.fromPath("${projectDir}/${params.default_additional_background}", checkIfExists:true)
+  }
+
+  if ( params.additional_mask ) {
       mask_ch = channel.fromPath("${params.additional_mask}", checkIfExists:true)
   } else {
       mask_ch = channel.fromPath("${projectDir}/${params.default_additional_mask}", checkIfExists:true)
   }
 
   fasta_ch = Channel.of(file("${params.fasta}", type: "file", checkIfExists:true))
 
-  squirrel(fasta_ch, refs_ch, mask_ch)
+  squirrel(fasta_ch, refs_ch, bg_ch, mask_ch)
 }

nextflow.config

@@ -40,7 +40,10 @@ params {
     concatenate = false
     clade = null
     run_phylo = false
+    run_apobec3_phylo = false
     include_background = false
+    additional_background = null
+    default_additional_background = "data/empty.fa"
     outgroups = null
 
     wf {
@@ -60,7 +63,7 @@ manifest {
     description     = 'Some QUIck Rearranging to Resolve Evolutionary Links.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = '1.0.7'
+    version         = '1.0.8'
 }
 
 executor {

nextflow_schema.json

@@ -22,11 +22,11 @@
         "clade": {
           "type": "string",
           "title": "Clade",
-          "description": "Specify whether the alignment is primarily for `cladei` or `cladeii`.",
+          "description": "Specify whether the alignment is primarily for 'cladei' or 'cladeii'.",
           "enum": [
             "cladei",
-	    "cladeia",
-	    "cladeib",
+	        "cladeia",
+	        "cladeib",
             "cladeii",
             "cladeiia",
             "cladeiib"
@@ -38,7 +38,7 @@
           "default": false,
           "title": "Run Sequence QC",
           "description": "Flag potentially problematic SNPs and sequences.",
-          "help_text": "Note that if run_phylo is also selected this additionally run qc based on the phylogenetic tree."
+          "help_text": "Note that if 'Run Phylo' is also selected this additionally runs qc based on the phylogenetic tree."
         },
         "additional_mask": {
           "type": "string",
@@ -51,25 +51,39 @@
           "type": "boolean",
           "default": false,
           "title": "Run Phylo",
-          "description": "Run phylogenetic reconstruction pipeline",
+          "description": "Run phylogenetics pipeline",
+          "help_text": ""
+        },
+        "run_apobec3_phylo": {
+          "type": "boolean",
+          "default": false,
+          "title": "Run APOBEC3 Phylo",
+          "description": "Run phylogenetics & APOBEC3-mutation reconstruction pipeline",
           "help_text": ""
         },
         "include_background": {
           "type": "boolean",
           "default": false,
           "title": "Include Background",
-          "description": "Include a default background set of sequences for the phylogenetics pipeline. Only the included outgroup sequences will be used, not those specified with `Outgroups`",
-          "help_text": "The set will be determined by the `--clade` specified."
+          "description": "Include a default background set of sequences for the phylogenetics pipeline. ",
+          "help_text": "The set will be determined by the `--clade` specified. Only the included outgroup sequences will be used, not those specified with 'Outgroups'."
+        },
+        "additional_background": {
+          "type": "string",
+          "format": "file-path",
+          "title": "Additional Background",
+          "description": "Include this additional FASTA file as background to the phylogenetics",
+          "help_text": ""
         },
         "outgroups": {
           "type": "string",
           "title": "Outgroups",
-          "description": "Specify which MPXV outgroup(s) in the alignment to use in the phylogeny. These must be in the input FASTA. Ignored if `Include Background` is selected.",
-          "help_text": "These are used only by the phylogenetics module and will get pruned out from the final tree."
+          "description": "Specify which MPXV outgroup(s) in the alignment to use in the phylogeny. ",
+          "help_text": "These are used only by the phylogenetics module and will get pruned out from the final tree. These must be in the input FASTA. Ignored if 'Include Background' is selected."
         },
         "assembly_refs": {
           "type": "string",
-          "format": "path",
+          "format": "file-path",
           "title": "Assembly References",
           "description": "References to check for `calls to reference` against, used only by the sequence QC process.",
           "help_text": ""