375 add spa type analysis to nanopore track (#395)

* add spa module to Makefile * add spatyper to S.aureus workflow * add spatyper to all configs * edit changelog * add spatyper module * inlude meatdata as input to spatyper * Add computational resources to spatyper * join input channels for spatyper * remove platform dependancy and add species dependancy --------- Co-authored-by: ryanjameskennedy <[email protected]> Co-authored-by: Ryan James Kennedy <[email protected]>
genomic-medicine-sweden · Feb 19, 2025 · 922fe79 · 922fe79
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added additional arguments for Resfinder when analysing Nanopore data
 - Added downloading of hostile index to `Makefile`
 - Added sw docs for `kpneumonia`, `spyogenes`, & `streptococcus`
+- Added module `spatyper` for typing of Spa gene in Staphylococcus aureus
 
 ### Fixed
 

diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -400,6 +400,13 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
 		ext.args = "--iontorrent --careful --sc"
 	}
+	withName: spatyper {
+		cpus = 2
+		memory = '2.GB'
+		container = "${params.containerDir}/spatyper.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spatyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
+	}
 	withName: tbprofiler_mergedb {
 		cpus = 16
 		memory = '12.GB'

diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
@@ -383,6 +383,13 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
 		ext.args = "--iontorrent --careful --sc"
 	}
+	withName: spatyper {
+		cpus = 2
+		memory = '2.GB'
+		container = "${params.containerDir}/spatyper.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spatyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
+	}
 	withName: tbprofiler_mergedb {
 		cpus = 4
 		memory = '12.GB'

diff --git a/configs/nextflow.cmd.config b/configs/nextflow.cmd.config
@@ -430,6 +430,13 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
 		ext.args = "--iontorrent --careful --sc"
 	}
+	withName: spatyper {
+		cpus = 2
+		memory = '2.GB'
+		container = "https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spatyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
+	}
 	withName: tbprofiler_mergedb {
 		cpus = 16
 		memory = '12.GB'

diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
@@ -413,6 +413,13 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
 		ext.args = "--iontorrent --careful --sc"
 	}
+	withName: spatyper {
+		cpus = 2
+		memory = '2.GB'
+		container = "${params.containerDir}/spatyper.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spatyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
+	}
 	withName: tbprofiler_mergedb {
 		cpus = params.cpus_large
 		memory = params.mem_medium

diff --git a/container/Makefile b/container/Makefile
@@ -46,6 +46,7 @@ remote_containers := ncbi-amrfinderplus.sif \
 					snippy.sif \
 					sourmash.sif \
 					spades.sif \
+					spatyper.sif \
 					tb-profiler.sif \
 					virulencefinder.sif
 
@@ -82,6 +83,7 @@ URL_skesa := https://depot.galaxyproject.org/singularity/skesa:2.5.1--hdcf5f25_0
 URL_snippy := https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2
 URL_sourmash := https://depot.galaxyproject.org/singularity/sourmash:4.8.2--hdfd78af_0
 URL_spades := https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1
+URL_spatyper := https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3
 URL_tb-profiler := https://depot.galaxyproject.org/singularity/tb-profiler:6.3.0--pyhdfd78af_0
 URL_virulencefinder := https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4--hdfd78af_1
 

diff --git a/nextflow-modules/modules/spatyper/main.nf b/nextflow-modules/modules/spatyper/main.nf
@@ -0,0 +1,41 @@
+process spatyper {
+  tag "${sample_id}"
+  scratch params.scratch
+
+  input:
+    tuple val(sample_id), path(assembly), val(platform)
+
+  output:
+    tuple val(sample_id), path(output), emit: tsv 
+    path "*versions.yml"              , emit: versions
+
+  when:
+      task.ext.when
+
+  script:
+    def args = task.ext.args ?: ''
+    output = "${sample_id}_spatyper.tsv"
+    """
+    spaTyper -f ${assembly} --output ${output} ${args}
+
+    cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
+    ${task.process}:
+     spatyper:
+      version: \$(echo \$(spaTyper --version 2>&1) | sed 's/spaTyper //p')
+      container: ${task.container}
+    END_VERSIONS
+    """
+
+  stub:
+    output = "${sample_id}_spatyper.tsv"
+    """
+    touch ${output}
+
+    cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
+    ${task.process}:
+     spatyper:
+      version: \$(echo \$(spatyper --version 2>&1) | sed 's/spaTyper //p')
+      container: ${task.container}
+    END_VERSIONS
+    """
+}
diff --git a/workflows/staphylococcus_aureus.nf b/workflows/staphylococcus_aureus.nf
@@ -20,6 +20,7 @@ include { mlst                                      } from '../nextflow-modules/
 include { resfinder                                 } from '../nextflow-modules/modules/resfinder/main.nf'
 include { samtools_index as samtools_index_assembly } from '../nextflow-modules/modules/samtools/main.nf'
 include { sccmec                                    } from '../nextflow-modules/modules/sccmec/main.nf'
+include { spatyper                                  } from '../nextflow-modules/modules/spatyper/main.nf'
 include { virulencefinder                           } from '../nextflow-modules/modules/virulencefinder/main.nf'
 include { CALL_BACTERIAL_BASE                       } from '../workflows/bacterial_base.nf'
 
@@ -93,6 +94,7 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         // TYPING
         mlst(ch_assembly, params.mlstScheme, pubMlstDb, mlstBlastDb)
         sccmec(ch_assembly)
+        spatyper(ch_assembly.join(ch_seqplat_meta))
 
         mask_polymorph_assembly.out.fasta
             .multiMap { sampleID, filePath -> 
@@ -173,6 +175,7 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         ch_versions = ch_versions.mix(resfinder.out.versions)
         ch_versions = ch_versions.mix(samtools_index_assembly.out.versions)
         ch_versions = ch_versions.mix(sccmec.out.versions)
+        ch_versions = ch_versions.mix(spatyper.out.versions)
         ch_versions = ch_versions.mix(virulencefinder.out.versions)
 
     emit: