Add sccmec module

CHANGELOG.md

@@ -21,9 +21,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added ska filepath to yaml
 - Added optional read downsampling using seqtk
 - Added `tbGradingRulesBed` to IGV track
-- Added module NanoPlot to check quality of raw reads from ONT
-- Added fastq as a process to `bacterial_base.nf`
-- Added hostile as a process to `bacterial_base.nf`
+- Added module `nanoplot` to check quality of raw reads from ONT
+- Added module `fastq` to check qc of strep samples
+- Added module `hostile` to remove human reads
+- Added module `sccmec` for typing of SCCmec cassettes in assemblies of Staphylococcus species
 
 ### Fixed
 

configs/nextflow.base.config

@@ -305,6 +305,10 @@ process {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
+	withName: sccmec {
+		container = "${params.containerDir}/sccmec.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+	}
 	withName: seqtk_sample {
 		container = "${params.containerDir}/seqtk.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/seqtk_sample", mode: 'copy', overwrite: true ]

configs/nextflow.ci.config

@@ -284,6 +284,10 @@ process {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
+	withName: sccmec {
+		container = "${params.containerDir}/sccmec.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+	}
 	withName: seqtk_sample {
 		container = "${params.containerDir}/seqtk.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/seqtk_sample", mode: 'copy', overwrite: true ]

configs/nextflow.dev.config

@@ -307,6 +307,10 @@ process {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
+	withName: sccmec {
+		container = "https://depot.galaxyproject.org/singularity/sccmec:1.2.0--hdfd78af_0"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+	}
 	withName: seqtk_sample {
 		container = "https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_2"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/seqtk_sample", mode: 'copy', overwrite: true ]

configs/nextflow.hopper.config

@@ -306,6 +306,10 @@ process {
 		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
+	withName: sccmec {
+		container = "https://depot.galaxyproject.org/singularity/sccmec:1.2.0--hdfd78af_0"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+	}
 	withName: seqtk_sample {
 		container = "https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_2"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/seqtk_sample", mode: 'copy', overwrite: true ]

configs/nextflow.ngp.config

@@ -313,6 +313,10 @@ process {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
+	withName: sccmec {
+		container = "${params.containerDir}/sccmec.sif"
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+	}
 	withName: seqtk_sample {
 		container = "${params.containerDir}/seqtk.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/seqtk_sample", mode: 'copy', overwrite: true ]

container/Makefile

@@ -35,6 +35,7 @@ remote_containers := ncbi-amrfinderplus.sif \
 					quast.sif \
 					resfinder.sif \
 					samtools.sif \
+					sccmec.sif \
 					seqtk.sif \
 					serotypefinder.sif \
 					shigapass.sif \
@@ -69,6 +70,7 @@ URL_perl-json := https://depot.galaxyproject.org/singularity/perl-json:4.10--pl5
 URL_quast := https://depot.galaxyproject.org/singularity/quast:5.2.0--py310pl5321hc8f18ef_2
 URL_resfinder := https://depot.galaxyproject.org/singularity/resfinder:4.4.2--pyhdfd78af_1
 URL_samtools := https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0
+URL_sccmec := https://depot.galaxyproject.org/singularity/sccmec:1.2.0--hdfd78af_0
 URL_seqtk := https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_2
 URL_serotypefinder := https://depot.galaxyproject.org/singularity/serotypefinder:2.0.2--py312hdfd78af_1
 URL_shigapass := https://depot.galaxyproject.org/singularity/shigapass:1.5.0--hdfd78af_0

nextflow-modules/modules/sccmec/main.nf

@@ -0,0 +1,40 @@
+process sccmec {
+  tag "${sample_id}"
+  scratch params.scratch
+
+  input:
+    tuple val(sample_id), path(assembly)
+
+  output:
+    tuple val(sample_id), path(output), emit: tsv 
+    path "*versions.yml"              , emit: versions
+
+  script:
+    def args = task.ext.args ?: ''
+    output = "${sample_id}_sccmec.tsv"
+    outputDir = "sccmec_outdir"
+    """
+    sccmec --input ${assembly} --prefix ${sample_id}_sccmec -o ${outputDir} ${args}
+    cp ${outputDir}/${sample_id}_sccmec.tsv ${output}
+
+    cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
+    ${task.process}:
+     sccmec:
+      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p')
+      container: ${task.container}
+    END_VERSIONS
+    """
+
+  stub:
+    output = "${sample_id}_sccmec.tsv"
+    """
+    touch ${output}
+
+    cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
+    ${task.process}:
+     sccmec:
+      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p')
+      container: ${task.container}
+    END_VERSIONS
+    """
+}

workflows/staphylococcus_aureus.nf

@@ -19,6 +19,7 @@ include { mask_polymorph_assembly                   } from '../nextflow-modules/
 include { mlst                                      } from '../nextflow-modules/modules/mlst/main.nf'
 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 { virulencefinder                           } from '../nextflow-modules/modules/virulencefinder/main.nf'
 include { CALL_BACTERIAL_BASE                       } from '../workflows/bacterial_base.nf'
 
@@ -90,6 +91,7 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
 
         // TYPING
         mlst(ch_assembly, params.mlstScheme, pubMlstDb, mlstBlastDb)
+        sccmec(ch_assembly)
 
         mask_polymorph_assembly.out.fasta
             .multiMap { sampleID, filePath -> 
@@ -167,6 +169,7 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         ch_versions = ch_versions.mix(mlst.out.versions)
         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(virulencefinder.out.versions)
 
     emit: