reintegrated shigeifinder

conf/modules.config

@@ -64,17 +64,16 @@ process {
         ]
     }
 
-    withName: SHIGATYPER {
-        ext.containers = params.shigatyper
-        //container = params.shigatyper.container
-        stageInMode = params.stage_in_mode
-        // scratch = false
-        publishDir = [
-            path: { "${params.outdir}/subtyping/shigatyper" },
-            mode: params.publish_dir_mode,
-        ]
-
-    }
+    //withName: SHIGATYPER {
+    //    ext.containers = params.shigatyper
+    //    //container = params.shigatyper.container
+    //    stageInMode = params.stage_in_mode
+    //    // scratch = false
+    //    publishDir = [
+    //        path: { "${params.outdir}/subtyping/shigatyper" },
+    //        mode: params.publish_dir_mode,
+    //    ]
+    //}
 
     //withName: FASTQSCAN {
     //    container = params.fastqscan.container
@@ -175,20 +174,20 @@ process {
         ]
     }
 
-    withName: SEQTK_FASTA_FASTQ {
-        ext.args = ""
-        ext.containers = params.seqtk
-        //container = params.seqtk.container
-        stageInMode = params.stage_in_mode
-        // scratch = false
-        publishDir = [
-            [
-                path: "${params.outdir}/subtyping/shigatyper",
-                mode: params.publish_dir_mode,
-                pattern: "*${params.seqtk.assembly_fastq}"
-            ]
-        ]
-    }
+    //withName: SEQTK_FASTA_FASTQ {
+    //    ext.args = ""
+    //    ext.containers = params.seqtk
+    //    //container = params.seqtk.container
+    //    stageInMode = params.stage_in_mode
+    //    // scratch = false
+    //    publishDir = [
+    //        [
+    //            path: "${params.outdir}/subtyping/shigatyper",
+    //            mode: params.publish_dir_mode,
+    //            pattern: "*${params.seqtk.assembly_fastq}"
+    //        ]
+    //    ]
+    //}
 
     withName: QUAST {
         //ext.args = params.quast.args
@@ -810,15 +809,15 @@ process {
         ]
     }
 
-    //withName: SHIGEIFINDER {
-    //    container = params.shigeifinder.container
-    //    stageInMode = params.stage_in_mode
-    //    scratch = false
-    //    publishDir = [
-    //        path: { "${params.outdir}/subtyping/shigeifinder" },
-    //        mode: params.publish_dir_mode,
-    //    ]
-    //}
+    withName: SHIGEIFINDER {
+        ext.containers = params.shigeifinder
+        stageInMode = params.stage_in_mode
+        scratch = false
+        publishDir = [
+            path: { "${params.outdir}/subtyping/shigeifinder" },
+            mode: params.publish_dir_mode,
+        ]
+    }
 
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {

docs/usage/configuration.md

@@ -650,10 +650,19 @@ Performa typing of *Staphylococcus* species.
     - header_p: Denotes if the output table of Lissero contains a header. Do not alter this field unless doing pipeline development.
 
 ### Shigeifinder
-Shigeifinder was added then removed. The code still remains but it will removed at a later date.
+*in-silico Shigella* typing. **NOTE:** It is unlikely this subtyper will be triggered as GTDB has merged *E.coli* and *Shigella* and updated sketch and updated ECTyper will be released soon to address the shortfalls of this sketch. If you are relying on *Shigella* detection add `--run_kraken true` to your command line or update the value in the `.nextflow.config` as Kraken2 (while slower) can still detect *Shigella*.
 
-### Shigatyper
-*in-silico Shigella* typing. **NOTE:** It is unlikely this subtyper will be triggered as GTDB has merged *E.coli* and *Shigella* and updated sketch and updated ECTyper will be released soon to address the shortfalls of this sketch.
+- shigeifinder
+    - singularity: The Singularity container containing Shigeifinder.
+    - docker: The path to the Docker container containing Shigeifinder.
+    - container_version: The version number **to be updated with the containers** as Shigeifinder does not currently have a version number tracked in the command.
+    - tsv_ext: Extension of output report.
+    - report_tag: The name of the output report for shigeifinder.
+    - header_p: Denotes that the output from Shigeifinder includes header values.
+
+
+### Shigatyper (Replaced with Shigeifinder)
+Code still reamins but it will likely be removed later on.
 
 - shigatyper
     - singularity: The Singularity container containing Shigatyper.

modules/local/shigatyper.nf

@@ -12,14 +12,15 @@ process SHIGATYPER{
     tuple val(meta), path(reads) // in mkkondo it will only work with assemblies
 
     output:
-    tuple val(meta), path("${prefix}${params.tsv_ext}"), emit: tsv
-    tuple val(meta), path("${prefix}-hits${params.tsv_ext}"), optional: true, emit: hits
+    tuple val(meta), path("${prefix}${params.shigatyper.tsv_ext}"), emit: tsv
+    tuple val(meta), path("${prefix}-hits${params.shigatyper.tsv_ext}"), optional: true, emit: hits
     path "versions.yml", emit: versions
 
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    export TMPDIR=\$PWD # set env temp dir to in the folder
     shigatyper $args --SE $reads --name $prefix
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/shigeifinder.nf

@@ -11,14 +11,14 @@ process SHIGEIFINDER {
     tuple val(meta), path(seqs)
 
     output:
-    tuple val(meta), path("*${params.shigeifinder}"), emit: tsv
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*${params.shigeifinder.tsv_ext}"), emit: tsv
+    path "versions.yml", emit: versions
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     tmp_file = "${prefix}.fa"
-    def VERSION = '1.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = params.shigeifinder.container_version // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     gunzip -c $seqs > $tmp_file
     shigeifinder $args --output ${prefix}.tsv -t $task.cpus -i $tmp_file

nextflow.config

@@ -588,23 +588,23 @@ params {
     }
 
     shigeifinder {
+        container_version = '1.3.2' // update version info with containers as it is not included in shigeifinder
         singularity = 'https://depot.galaxyproject.org/singularity/shigeifinder:1.3.2--pyhdfd78af_0'
         docker = 'quay.io/biocontainers/shigeifinder:1.3.2--pyhdfd78af_0'
         tsv_ext = ".tsv"
         //shigeifinder_search = "Shigella"
-        //report_tag = params.subtyping_report.report_tag
-        //report_tag = "ShigeiFinder"
+        report_tag = "Shigeifinder${params.subtyping_report.report_tag}"
         header_p = true
     }
 
-    shigatyper {
-        singularity = 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0'
-        docker = 'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0'
-        tsv_ext = ".tsv"
-        report_tag = "ShigaTyper${params.subtyping_report.report_tag}"
-        //report_tag = params.subtyping_report.report_tag
-        header_p = true
-    }
+    //shigatyper {
+    //    singularity = 'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0'
+    //    docker = 'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0'
+    //    tsv_ext = ".tsv"
+    //    report_tag = "ShigaTyper${params.subtyping_report.report_tag}"
+    //    //report_tag = params.subtyping_report.report_tag
+    //    header_p = true
+    //}
 
     kraken_bin {
         // Python only

subworkflows/local/subtype_genome.nf

@@ -13,9 +13,9 @@ This creates an output similar to the kraken report
 include { ECTYPER } from "../../modules/local/ectyper.nf"
 include { SISTR } from "../../modules/local/sistr.nf"
 include { LISSERO } from "../../modules/local/lissero.nf"
-//include { SHIGEIFINDER } from "../../modules/local/shigeifinder.nf"
-include { SHIGATYPER } from "../../modules/local/shigatyper.nf"
-include { SEQTK_FASTA_FASTQ } from "../../modules/local/seqtk_fasta_fastq.nf"
+include { SHIGEIFINDER } from "../../modules/local/shigeifinder.nf"
+//include { SHIGATYPER } from "../../modules/local/shigatyper.nf"
+//include { SEQTK_FASTA_FASTQ } from "../../modules/local/seqtk_fasta_fastq.nf"
 include { KLEBORATE } from "../../modules/local/kleborate.nf"
 include { SPATYPER } from "../../modules/local/spatyper.nf"
 
@@ -60,11 +60,16 @@ workflow SUBTYPE_GENOME{
         meta, result, contigs -> tuple(meta, contigs)
     })
 
-    //shigatyper requries reads only
-    fastq_reads = SEQTK_FASTA_FASTQ(isolates.shigella.map{
+
+    shigeifinder_results = SHIGEIFINDER(isolates.shigella.map{
         meta, result, contigs -> tuple(meta, contigs)
     })
-    shigatyper_results = SHIGATYPER(fastq_reads.fastq_reads)
+
+    //shigatyper requries reads onl
+    //fastq_reads = SEQTK_FASTA_FASTQ(isolates.shigella.map{
+    //    meta, result, contigs -> tuple(meta, contigs)
+    //})
+    //shigatyper_results = SHIGATYPER(fastq_reads.fastq_reads)
 
     kleborate_results = KLEBORATE(isolates.klebsiella.map{
         meta, result, contigs -> tuple(meta, contigs)
@@ -84,8 +89,8 @@ workflow SUBTYPE_GENOME{
                 ECTYPER.out.versions,
                 SISTR.out.versions,
                 LISSERO.out.versions,
-                //SHIGEIFINDER.out.versions)
-                SHIGATYPER.out.versions)
+                SHIGEIFINDER.out.versions)
+                //SHIGATYPER.out.versions)
 
     isolates.fallthrough.subscribe{
         log.info "Sample ${it[0].id} could not be serotyped, sample identified as: ${it[1]}"
@@ -97,8 +102,8 @@ workflow SUBTYPE_GENOME{
         add_report_tag(ec_typer_results.tsv, params.ectyper),
         add_report_tag(sistr_results.tsv, params.sistr),
         add_report_tag(lissero_results.tsv, params.lissero),
-        //add_report_tag(shigeifinder_results.tsv, params.shigeifinder))
-        add_report_tag(shigatyper_results.tsv, params.shigeifinder))
+        add_report_tag(shigeifinder_results.tsv, params.shigeifinder))
+        //add_report_tag(shigatyper_results.tsv, params.shigeifinder))
 
     emit:
     reports = reports