Merge branch 'nf-core:dev' into diamond-update

conf/modules.config

@@ -145,7 +145,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/filtlong" },
             mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
+            pattern: '*.{fastq.gz,log}',
             enabled: params.save_preprocessed_reads
         ]
     }
@@ -347,6 +347,7 @@ process {
     }
 
     withName: CENTRIFUGE_KREPORT {
+        errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
@@ -398,6 +399,13 @@ process {
         ]
     }
 
+    withName: MOTUS_MERGE {
+        publishDir = [
+            path: { "${params.outdir}/motus/" },
+            mode: params.publish_dir_mode
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

conf/test_motus.config

@@ -38,4 +38,5 @@ params {
     run_centrifuge                        = false
     run_diamond                           = false
     run_motus                             = true
+    run_profile_standardisation           = true
 }

modules.json

@@ -22,7 +22,7 @@
                 "git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
             },
             "centrifuge/kreport": {
-                "git_sha": "be4ae28c3c95b3c4047a7d9fb4cb0ed749631cea"
+                "git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
             },
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -37,7 +37,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "filtlong": {
-                "git_sha": "089f761f0bf79c4a486f1df9b6205f650196a2c1"
+                "git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
             },
             "gunzip": {
                 "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
@@ -78,6 +78,9 @@
             "minimap2/index": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "motus/merge": {
+                "git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
+            },
             "motus/profile": {
                 "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
             },

modules/nf-core/modules/centrifuge/kreport/main.nf

@@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
         'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
 
     input:
-    tuple val(meta), path(results)
+    tuple val(meta), path(report)
     path db
 
     output:
@@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
-    centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
+    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/modules/centrifuge/kreport/meta.yml

@@ -15,9 +15,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - results:
+  - report:
       type: file
-      description: File containing the centrifuge classification results
+      description: File containing the centrifuge classification report
       pattern: "*.{txt}"
 
 output:

modules/nf-core/modules/filtlong/main.nf

@@ -12,7 +12,8 @@ process FILTLONG {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
-    path "versions.yml"                                     , emit: versions
+    tuple val(meta), path("*.log")     , emit: log
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,6 +28,7 @@ process FILTLONG {
         $short_reads \\
         $args \\
         $longreads \\
+        2> ${prefix}.log \\
         | gzip -n > ${prefix}.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/modules/filtlong/meta.yml

@@ -45,6 +45,11 @@ output:
       type: file
       description: Filtered (compressed) fastq file
       pattern: "*.fastq.gz"
+  - log:
+      type: file
+      description: Standard error logging file containing summary statistics
+      pattern: "*.log"
 
 authors:
   - "@d4straub"
+  - "@sofstam"

modules/nf-core/modules/motus/merge/main.nf

@@ -0,0 +1,47 @@
+VERSION = '3.0.1'
+
+process MOTUS_MERGE {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
+        'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
+
+    input:
+    path input
+    path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
+    path profile_version_yml, stageAs: 'profile_version.yml'
+    val biom_format
+
+    output:
+    path("*.txt") , optional: true, emit: txt
+    path("*.biom"), optional: true, emit: biom
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = 'motus_merged'
+    def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
+    def output = biom_format ? "-B -o ${prefix}.biom" : "-o ${prefix}.txt"
+    """
+    motus \\
+        merge \\
+        -db $db \\
+        ${cmd_input} \\
+        $args \\
+        ${output}
+
+    ## Take version from the mOTUs/profile module output, as cannot reconstruct
+    ## version without having database staged in this directory.
+    VERSION=\$(cat ${profile_version_yml} | grep '/*motus:.*' | sed 's/.*otus: //g')
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        motus: \$VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/modules/motus/merge/meta.yml

@@ -0,0 +1,57 @@
+name: "motus_merge"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+  - merging
+  - merge
+  - otu table
+tools:
+  - "motus":
+      description: "Marker gene-based OTU (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1038/s41467-019-08844-4"
+      licence: "['GPL v3']"
+
+input:
+  - input:
+      type: file
+      description: |
+        List of output files (more than one) from motus profile,
+        or a single directory containing motus output files.
+  - db:
+      type: directory
+      description: |
+        mOTUs database downloaded by `motus downloadDB`
+        pattern: "db_mOTU/"
+  - profile_version_yml:
+      type: file
+      description: |
+        A single versions.yml file output from motus/profile. motus/merge cannot reconstruct
+        this itself without having the motus database present and configured with the tool
+        so here we take it from what is already reported by the upstream module.
+      pattern: "versions.yml"
+  - biom_format:
+      type: boolean
+      description: Whether to save output OTU table in biom format
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - txt:
+      type: file
+      description: OTU table in txt format, if BIOM format not requested
+      pattern: "*.txt"
+  - biom:
+      type: file
+      description: OTU table in biom format, if BIOM format requested
+      pattern: "*.biom"
+
+authors:
+  - "@jfy133"

nextflow.config

@@ -132,6 +132,10 @@ params {
     // krona
     run_krona                  = false
     krona_taxonomy_directory   = null
+
+    // profile standardisation
+    run_profile_standardisation = false
+    generate_biom_output                 = false
 }
 
 // Load base.config by default for all pipelines

nextflow_schema.json

@@ -52,7 +52,8 @@
                     "type": "string",
                     "description": "Name of iGenomes reference.",
                     "fa_icon": "fas fa-book",
-                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
+                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
+                    "hidden": true
                 },
                 "igenomes_base": {
                     "type": "string",
@@ -444,7 +445,13 @@
         },
         "krona_taxonomy_directory": {
             "type": "string",
-            "default": null
+            "default": "None"
+        },
+        "run_profile_standardisation": {
+            "type": "boolean"
+        },
+        "generate_biom_output": {
+            "type": "boolean"
         }
     }
 }

subworkflows/local/longread_preprocessing.nf

@@ -30,6 +30,7 @@ workflow LONGREAD_PREPROCESSING {
 
         ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
 
     } else {
         PORECHOP ( reads )
@@ -45,6 +46,7 @@ workflow LONGREAD_PREPROCESSING {
 
         ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
         ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
 
     }
 

subworkflows/local/profiling.nf

@@ -110,7 +110,7 @@ workflow PROFILING {
                                 }
 
         MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary )
-        ch_multiqc_files       = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([])  )
+        ch_multiqc_files       = ch_multiqc_files.mix( MALT_RUN.out.log )
         ch_versions            = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan )
         ch_raw_profiles        = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt )
@@ -127,7 +127,7 @@ workflow PROFILING {
                                 }
 
         KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
-        ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([])  )
+        ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
         ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
         ch_raw_profiles        = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
@@ -148,7 +148,7 @@ workflow PROFILING {
                                 }
 
         CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads  )
-        CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
+        CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.report, ch_input_for_centrifuge.db)
         ch_versions            = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
         ch_raw_profiles        = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
@@ -185,7 +185,7 @@ workflow PROFILING {
 
         KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
         KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name)
-        ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([])  )
+        ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary  )
         ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
         ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
@@ -228,13 +228,13 @@ workflow PROFILING {
         MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
         ch_versions        = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
-        ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
-
+        ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
     }
 
     emit:
     classifications = ch_raw_classifications
     profiles        = ch_raw_profiles    // channel: [ val(meta), [ reads ] ] - should be text files or biom
     versions        = ch_versions          // channel: [ versions.yml ]
+    motus_version    = params.run_motus ? MOTUS_PROFILE.out.versions.first() : Channel.empty()
     mqc             = ch_multiqc_files
 }

subworkflows/local/standardisation_profiles.nf

@@ -0,0 +1,56 @@
+//
+// Create Krona visualizations
+//
+
+include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main'
+
+workflow STANDARDISATION_PROFILES {
+    take:
+    classifications
+    profiles
+    databases
+    motu_version
+
+    main:
+    ch_standardised_tables = Channel.empty()
+    ch_versions            = Channel.empty()
+
+    /*
+        Split profile results based on tool they come from
+    */
+    ch_input_profiles = profiles
+        .branch {
+            motus: it[0]['tool'] == 'motus'
+            unknown: true
+        }
+
+    ch_input_classifications = classifications
+        .branch {
+            unknown: true
+        }
+
+    ch_input_databases = databases
+        .branch {
+            motus: it[0]['tool'] == 'motus'
+            unknown: true
+        }
+
+    /*
+        Standardise and aggregate
+    */
+
+    // mOTUs has a 'single' database, and cannot create custom ones.
+    // Therefore removing db info here, and publish merged at root mOTUs results
+    // directory
+    MOTUS_MERGE ( ch_input_profiles.motus.map{it[1]}.collect(), ch_input_databases.motus.map{it[1]}, motu_version, params.generate_biom_output )
+    if ( params.generate_biom_output ) {
+        ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
+    } else {
+        ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
+    }
+    ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
+
+    emit:
+    tables = ch_standardised_tables
+    versions = ch_versions
+}

subworkflows/local/visualization_krona.nf

@@ -78,7 +78,7 @@ workflow VISUALIZATION_KRONA {
     ch_krona_text_for_import = ch_cleaned_krona_text
         .map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
         .groupTuple()
-        .dump(tag: "text")
+
     KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
     ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
     ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
@@ -92,7 +92,7 @@ workflow VISUALIZATION_KRONA {
         ch_krona_taxonomy_for_input = GUNZIP.out.gunzip
             .map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
             .groupTuple()
-            .dump(tag: "taxonomy")
+
         KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) )
         ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html )
         ch_versions = ch_versions.mix( MEGAN_RMA2INFO.out.versions.first() )

workflows/taxprofiler.nf

@@ -65,6 +65,7 @@ include { LONGREAD_HOSTREMOVAL          } from '../subworkflows/local/longread_h
 include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
 include { PROFILING                     } from '../subworkflows/local/profiling'
 include { VISUALIZATION_KRONA           } from '../subworkflows/local/visualization_krona'
+include { STANDARDISATION_PROFILES      } from '../subworkflows/local/standardisation_profiles'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -220,6 +221,14 @@ workflow TAXPROFILER {
         ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
     }
 
+    /*
+        SUBWORKFLOW: PROFILING STANDARDISATION
+    */
+    if ( params.run_profile_standardisation ) {
+        STANDARDISATION_PROFILES ( PROFILING.out.classifications, PROFILING.out.profiles, DB_CHECK.out.dbs, PROFILING.out.motus_version )
+        ch_versions = ch_versions.mix( STANDARDISATION_PROFILES.out.versions )
+    }
+
     /*
         MODULE: MultiQC
     */
@@ -257,7 +266,7 @@ workflow TAXPROFILER {
         ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
     }
 
-    ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
+    ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
 
     // TODO create multiQC module for metaphlan
     MULTIQC (