Module update

modules.json

@@ -3,104 +3,140 @@
     "homePage": "https://github.com/nf-core/taxprofiler",
     "repos": {
         "nf-core/modules": {
+            "git_url": "https://github.com/nf-core/modules.git",
+            "modules": {
                 "adapterremoval": {
+                    "branch": "master",
                     "git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
                 },
                 "bbmap/bbduk": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "branch": "master",
+                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
                 },
                 "bowtie2/align": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "branch": "master",
+                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
                 },
                 "bowtie2/build": {
+                    "branch": "master",
                     "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "cat/fastq": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "branch": "master",
+                    "git_sha": "b034029b59b1198075da8019074bc02051a6100e"
                 },
                 "centrifuge/centrifuge": {
+                    "branch": "master",
                     "git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
                 },
                 "centrifuge/kreport": {
+                    "branch": "master",
                     "git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
                 },
                 "custom/dumpsoftwareversions": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "diamond/blastx": {
+                    "branch": "master",
                     "git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
                 },
                 "fastp": {
-                "git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
+                    "branch": "master",
+                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
                 },
                 "fastqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "branch": "master",
+                    "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
                 },
                 "filtlong": {
+                    "branch": "master",
                     "git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
                 },
                 "gunzip": {
-                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
+                    "branch": "master",
+                    "git_sha": "fa37e0662690c4ec4260dae282fbce08777503e6"
                 },
                 "kaiju/kaiju": {
+                    "branch": "master",
                     "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
                 },
                 "kaiju/kaiju2krona": {
+                    "branch": "master",
                     "git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
                 },
                 "kaiju/kaiju2table": {
+                    "branch": "master",
                     "git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
                 },
                 "kraken2/kraken2": {
-                "git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
+                    "branch": "master",
+                    "git_sha": "409a308ba46284d8ebb48c2c1befd6f6433db3f7"
                 },
                 "krakentools/kreport2krona": {
-                "git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
+                    "branch": "master",
+                    "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
                 },
                 "krona/ktimporttaxonomy": {
+                    "branch": "master",
                     "git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
                 },
                 "krona/ktimporttext": {
+                    "branch": "master",
                     "git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
                 },
                 "malt/run": {
+                    "branch": "master",
                     "git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
                 },
                 "megan/rma2info": {
+                    "branch": "master",
                     "git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
                 },
-            "metaphlan3": {
+                "metaphlan3/metaphlan3": {
-                "git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"
+                    "branch": "master",
+                    "git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"
                 },
                 "minimap2/align": {
+                    "branch": "master",
                     "git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
                 },
                 "minimap2/index": {
+                    "branch": "master",
                     "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "motus/merge": {
+                    "branch": "master",
                     "git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
                 },
                 "motus/profile": {
+                    "branch": "master",
                     "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
                 },
                 "multiqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                    "branch": "master",
+                    "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
                 },
                 "porechop": {
+                    "branch": "master",
                     "git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
                 },
                 "prinseqplusplus": {
+                    "branch": "master",
                     "git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
                 },
                 "samtools/bam2fq": {
+                    "branch": "master",
                     "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
                 },
                 "samtools/view": {
-                "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "untar": {
-                "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
+                }
             }
         }
     }

modules/nf-core/modules/bbmap/bbduk/meta.yml

@@ -4,6 +4,7 @@ keywords:
   - trimming
   - adapter trimming
   - quality trimming
+  - fastq
 tools:
   - bbmap:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.

modules/nf-core/modules/bowtie2/align/main.nf

@@ -1,67 +1,62 @@
 process BOWTIE2_ALIGN {
     tag "$meta.id"
-    label 'process_high'
+    label "process_high"
 
-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
+    conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
+        "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
+        "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
 
     input:
     tuple val(meta), path(reads)
     path  index
     val   save_unaligned
+    val   sort_bam
 
     output:
-    tuple val(meta), path('*.bam')    , emit: bam
+    tuple val(meta), path("*.bam")    , emit: bam
-    tuple val(meta), path('*.log')    , emit: log
+    tuple val(meta), path("*.log")    , emit: log
-    tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
+    tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
     path  "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args = task.ext.args ?: ""
-    def args2 = task.ext.args2 ?: ''
+    def args2 = task.ext.args2 ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
-        """
-        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
-        bowtie2 \\
-            -x \$INDEX \\
-            -U $reads \\
-            --threads $task.cpus \\
-            $unaligned \\
-            $args \\
-            2> ${prefix}.bowtie2.log \\
-            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
 
-        cat <<-END_VERSIONS > versions.yml
+    def unaligned = ""
-        "${task.process}":
+    def reads_args = ""
-            bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+    if (meta.single_end) {
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+        reads_args = "-U ${reads}"
-        END_VERSIONS
-        """
     } else {
-        def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
+        reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
+    }
+
+    def samtools_command = sort_bam ? 'sort' : 'view'
+
     """
-        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+    INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
+    [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
+    [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
+
     bowtie2 \\
         -x \$INDEX \\
-            -1 ${reads[0]} \\
+        $reads_args \\
-            -2 ${reads[1]} \\
         --threads $task.cpus \\
         $unaligned \\
         $args \\
         2> ${prefix}.bowtie2.log \\
-            | samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
+        | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
 
     if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
         mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
     fi
+
     if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
         mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
     fi
@@ -73,5 +68,4 @@ process BOWTIE2_ALIGN {
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
-    }
 }

modules/nf-core/modules/bowtie2/align/meta.yml

@@ -2,7 +2,9 @@ name: bowtie2_align
 description: Align reads to a reference genome using bowtie2
 keywords:
   - align
+  - map
   - fasta
+  - fastq
   - genome
   - reference
 tools:
@@ -29,6 +31,15 @@ input:
       type: file
       description: Bowtie2 genome index files
       pattern: "*.ebwt"
+  - save_unaligned:
+      type: boolean
+      description: |
+        Save reads that do not map to the reference (true) or discard them (false)
+        (default: false)
+  - sort_bam:
+      type: boolean
+      description: use samtools sort (true) or samtools view (false)
+      pattern: "true or false"
 output:
   - bam:
       type: file

modules/nf-core/modules/cat/fastq/main.nf

@@ -4,8 +4,8 @@ process CAT_FASTQ {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
@@ -48,4 +48,33 @@ process CAT_FASTQ {
             """
         }
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def readList = reads.collect{ it.toString() }
+    if (meta.single_end) {
+        if (readList.size > 1) {
+            """
+            touch ${prefix}.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    } else {
+        if (readList.size > 2) {
+            """
+            touch ${prefix}_1.merged.fastq.gz
+            touch ${prefix}_2.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    }
+
 }

modules/nf-core/modules/custom/dumpsoftwareversions/main.nf

@@ -1,11 +1,11 @@
 process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_low'
+    label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
 
     input:
     path versions

modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python
 
+import yaml
 import platform
 from textwrap import dedent
 
-import yaml
-
 
 def _make_versions_html(versions):
     html = [
@@ -59,8 +58,7 @@ versions_by_module = {}
 for process, process_versions in versions_by_process.items():
     module = process.split(":")[-1]
     try:
-        if versions_by_module[module] != process_versions:
+        assert versions_by_module[module] == process_versions, (
-            raise AssertionError(
             "We assume that software versions are the same between all modules. "
             "If you see this error-message it means you discovered an edge-case "
             "and should open an issue in nf-core/tools. "

modules/nf-core/modules/fastp/main.nf

@@ -13,7 +13,7 @@ process FASTP {
     val   save_merged
 
     output:
-    tuple val(meta), path('*.trim.fastq.gz')  , optional:true, emit: reads
+    tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
     tuple val(meta), path('*.json')           , emit: json
     tuple val(meta), path('*.html')           , emit: html
     tuple val(meta), path('*.log')            , emit: log
@@ -28,19 +28,23 @@ process FASTP {
     def args = task.ext.args ?: ''
     // Added soft-links to original fastqs for consistent naming in MultiQC
     def prefix = task.ext.prefix ?: "${meta.id}"
+    // Use single ended for interleaved. Add --interleaved_in in config.
     if (meta.single_end) {
         def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
         """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
+        [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
-        fastp \\
+        cat ${prefix}.fastq.gz \\
+        | fastp \\
+            --stdin \\
+            --stdout \\
             --in1 ${prefix}.fastq.gz \\
-            --out1 ${prefix}.trim.fastq.gz \\
             --thread $task.cpus \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
             $fail_fastq \\
             $args \\
-            2> ${prefix}.fastp.log
+            2> ${prefix}.fastp.log \\
+        | gzip -c > ${prefix}.fastp.fastq.gz
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
@@ -50,13 +54,13 @@ process FASTP {
         def fail_fastq  = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
         def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
         """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
         fastp \\
             --in1 ${prefix}_1.fastq.gz \\
             --in2 ${prefix}_2.fastq.gz \\
-            --out1 ${prefix}_1.trim.fastq.gz \\
+            --out1 ${prefix}_1.fastp.fastq.gz \\
-            --out2 ${prefix}_2.trim.fastq.gz \\
+            --out2 ${prefix}_2.fastp.fastq.gz \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
             $fail_fastq \\

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

@@ -15,7 +15,7 @@ input:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
+        Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.
         e.g. [ id:'test', single_end:false ]
   - reads:
       type: file
@@ -38,7 +38,7 @@ output:
   - reads:
       type: file
       description: The trimmed/modified/unmerged fastq reads
-      pattern: "*trim.fastq.gz"
+      pattern: "*fastp.fastq.gz"
   - json:
       type: file
       description: Results in JSON format

modules/nf-core/modules/fastqc/main.nf

@@ -44,4 +44,16 @@ process FASTQC {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/gunzip/main.nf

@@ -31,4 +31,14 @@ process GUNZIP {
         gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    gunzip = archive.toString() - '.gz'
+    """
+    touch $gunzip
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
 }

modules/nf-core/modules/kraken2/kraken2/main.nf

@@ -14,9 +14,9 @@ process KRAKEN2_KRAKEN2 {
     val save_reads_assignment
 
     output:
-    tuple val(meta), path('*classified*')     , optional:true, emit: classified_reads_fastq
+    tuple val(meta), path('*.classified{.,_}*')     , optional:true, emit: classified_reads_fastq
-    tuple val(meta), path('*unclassified*')   , optional:true, emit: unclassified_reads_fastq
+    tuple val(meta), path('*.unclassified{.,_}*')   , optional:true, emit: unclassified_reads_fastq
-    tuple val(meta), path('*classifiedreads*'), optional:true, emit: classified_reads_assignment
+    tuple val(meta), path('*classifiedreads.txt')   , optional:true, emit: classified_reads_assignment
     tuple val(meta), path('*report.txt')                           , emit: report
     path "versions.yml"                                            , emit: versions
 
@@ -29,9 +29,9 @@ process KRAKEN2_KRAKEN2 {
     def paired       = meta.single_end ? "" : "--paired"
     def classified   = meta.single_end ? "${prefix}.classified.fastq"   : "${prefix}.classified#.fastq"
     def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
-    def classified_command = save_output_fastqs ? "--classified-out ${classified}" : ""
+    def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
-    def unclassified_command = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
+    def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
-    def readclassification_command = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
+    def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : ""
     def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
 
     """
@@ -40,9 +40,9 @@ process KRAKEN2_KRAKEN2 {
         --threads $task.cpus \\
         --report ${prefix}.kraken2.report.txt \\
         --gzip-compressed \\
-        $unclassified_command \\
+        $unclassified_option \\
-        $classified_command \\
+        $classified_option \\
-        $readclassification_command \\
+        $readclassification_option \\
         $paired \\
         $args \\
         $reads

modules/nf-core/modules/krakentools/kreport2krona/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.2' // Version information not provided by tool on CLI
-
 process KRAKENTOOLS_KREPORT2KRONA {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
@@ -22,6 +21,7 @@ process KRAKENTOOLS_KREPORT2KRONA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     kreport2krona.py \\
         -r ${kreport} \\

modules/nf-core/modules/metaphlan3/metaphlan3/main.nf

@@ -28,15 +28,18 @@ process METAPHLAN3 {
     def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
 
     """
+    BT2_DB=`find -L "${metaphlan_db}" -name "*rev.1.bt2" -exec dirname {} \\;`
+
     metaphlan \\
         --nproc $task.cpus \\
         $input_type \\
         $input_data \\
         $args \\
         $bowtie2_out \\
-        --bowtie2db ${metaphlan_db} \\
+        --bowtie2db \$BT2_DB \\
         --biom ${prefix}.biom \\
         --output_file ${prefix}_profile.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')

modules/nf-core/modules/metaphlan3/metaphlan3/meta.yml

@@ -24,6 +24,12 @@ input:
       type: file
       description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
       pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
+  - metaphlan_db:
+      type: file
+      description: |
+        Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.
+        Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!
+      pattern: "*/"
 
 output:
   - meta:

modules/nf-core/modules/multiqc/main.nf

@@ -1,13 +1,14 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
 
     input:
-    path multiqc_files
+    path  multiqc_files, stageAs: "?/*"
+    tuple path(multiqc_config), path(multiqc_logo)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -20,8 +21,25 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
     """
-    multiqc -f $args .
+    multiqc \\
+        --force \\
+        $config \\
+        $args \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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

@@ -17,6 +17,14 @@ input:
       type: file
       description: |
         List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Logo file for MultiQC
+      pattern: "*.{png}"
 output:
   - report:
       type: file

modules/nf-core/modules/samtools/view/main.nf

@@ -1,6 +1,6 @@
 process SAMTOOLS_VIEW {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/modules/untar/main.nf

@@ -1,11 +1,11 @@
 process UNTAR {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)
@@ -21,12 +21,29 @@ process UNTAR {
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     untar     = archive.toString() - '.tar.gz'
+
     """
+    mkdir output
+
     tar \\
+        -C output --strip-components 1 \\
         -xzvf \\
         $args \\
         $archive \\
-        $args2 \\
+        $args2
+
+    mv output ${untar}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    untar     = archive.toString() - '.tar.gz'
+    """
+    touch $untar
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

subworkflows/local/profiling.nf

@@ -7,7 +7,7 @@ include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV  } from '../../modules/nf-core/mo
 include { KRAKEN2_KRAKEN2                       } from '../../modules/nf-core/modules/kraken2/kraken2/main'
 include { CENTRIFUGE_CENTRIFUGE                 } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
 include { CENTRIFUGE_KREPORT                    } from '../../modules/nf-core/modules/centrifuge/kreport/main'
-include { METAPHLAN3                            } from '../../modules/nf-core/modules/metaphlan3/main'
+include { METAPHLAN3                            } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
 include { KAIJU_KAIJU                           } from '../../modules/nf-core/modules/kaiju/kaiju/main'
 include { KAIJU_KAIJU2TABLE                     } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
 include { DIAMOND_BLASTX                        } from '../../modules/nf-core/modules/diamond/blastx/main'

subworkflows/local/shortread_hostremoval.nf

@@ -22,7 +22,7 @@ workflow SHORTREAD_HOSTREMOVAL {
         ch_bowtie2_index = index.first()
     }
 
-    BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true )
+    BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true, false )
     ch_versions      = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
     ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
 

workflows/taxprofiler.nf

@@ -269,7 +269,7 @@ workflow TAXPROFILER {
 
     // TODO create multiQC module for metaphlan
     MULTIQC (
-        ch_multiqc_files.collect()
+        ch_multiqc_files.collect(), [[], []]
     )
     multiqc_report = MULTIQC.out.report.toList()
     ch_versions    = ch_versions.mix(MULTIQC.out.versions)