nf-core · jfy133 · Nov 30, 2023 · Nov 9, 2023 · Nov 10, 2023 · Nov 13, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.2dev - Bouncy Basenji [unreleased]
+
+### `Added`
+
+- [#417](https://github.com/nf-core/taxprofiler/pull/417) - Added reference-free metagenome estimation with Nonpareil (added by @jfy133)
+
+### `Fixed`
+
+### `Dependencies`
+
+| Tool    | Previous version | New version |
+| ------- | ---------------- | ----------- |
+| multiqc | 1.15             | 1.18        |
+
+### `Deprecated`
+
 ## v1.1.2 - Augmented Akita Patch [2023-10-27]
 
 ### `Added`

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -30,6 +30,10 @@
 
   > Schubert, M., Lindgreen, S., & Orlando, L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 9, 88. https://doi.org/10.1186/s13104-016-1900-2
 
+- [Nonpareil](https://doi.org/10.1128/mSystems.00039-18)
+
+  - Rodriguez-R, L. M., Gunturu, S., Tiedje, J. M., Cole, J. R., & Konstantinidis, K. T. (2018). Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity. mSystems, 3(3). https://doi.org/10.1128/mSystems.00039-18
+
 - [Porechop](https://github.com/rrwick/Porechop)
 
   > Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017). Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial Genomics, 3(10), e000132. https://doi.org/10.1099/mgen.0.000132

diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@
    - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong))
    - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))
    - Run merging
-3. Supports statistics for host-read removal ([Samtools](http://www.htslib.org/))
+3. Supports statistics metagenome coverage estimation ([Nonpareil](https://nonpareil.readthedocs.io/en/latest/)) and for host-read removal ([Samtools](http://www.htslib.org/))
 4. Performs taxonomic classification and/or profiling using one or more of:
    - [Kraken2](https://ccb.jhu.edu/software/kraken2/)
    - [MetaPhlAn](https://huttenhower.sph.harvard.edu/metaphlan/)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -10,6 +10,44 @@ report_section_order:
     order: -1001
   "nf-core-taxprofiler-summary":
     order: -1002
+  general_stats":
+    order: 1000
+  fastqc:
+    order: 900
+  fastqc-1:
+    order: 800
+  fastp:
+    order: 700
+  adapterRemoval:
+    order: 600
+  nonpareil_all_samples:
+    order: 500
+  porechop:
+    order: 400
+  bbduk:
+    order: 300
+  prinseqplusplus:
+    order: 200
+  filtlong:
+    order: 100
+  bowtie2:
+    order: 90
+  samtools:
+    order: 80
+  kraken:
+    order: 70
+  bracken:
+    order: 60
+  centrifuge:
+    order: 50
+  malt:
+    order: 40
+  diamond:
+    order: 30
+  kaiju:
+    order: 20
+  motus:
+    order: 10
 
 export_plots: true
 
@@ -21,6 +59,7 @@ run_modules:
   - fastqc
   - adapterRemoval
   - fastp
+  - custom_content
   - bbduk
   - prinseqplusplus
   - porechop
@@ -33,7 +72,6 @@ run_modules:
   - diamond
   - malt
   - motus
-  - custom_content
 
 sp:
   diamond:
@@ -42,6 +80,13 @@ sp:
     fn_re: ".*(fastqc|falco)_data.txt$"
   fastqc/zip:
     fn: "*_fastqc.zip"
+  nonpareil_all_samples_mqc:
+    fn: "nonpareil_all_samples_mqc.png"
+
+custom_data:
+  nonpareil_all_samples:
+    section_name: "Nonpareil"
+    description: "Nonpareil uses the redundancy of the reads in metagenomic datasets to estimate the average coverage and predict the amount of sequences that will be required to achieve “nearly complete coverage”. Plots here are not interactive - being exported directly from the tool. If you have difficulty reading the plot, please see the individual PNG files in the results directory. DOI: https://doi.org/10.1128/mSystems.00039-18"
 
 top_modules:
   - "fastqc":
@@ -58,13 +103,8 @@ top_modules:
       path_filters_exclude:
         - "*raw*"
       extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
-  - "fastp"
-  - "adapterRemoval"
   - "porechop":
       extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated."
-  - "bbduk"
-  - "prinseqplusplus"
-  - "filtlong"
   - "bowtie2":
       name: "bowtie2"
   - "samtools":
@@ -93,12 +133,11 @@ top_modules:
         - "*.centrifuge.txt"
   - "malt":
       name: "MALT"
-  - "diamond"
   - "kaiju":
       name: "Kaiju"
-  - "motus"
 
-#It is not possible to set placement for custom kraken and centrifuge columns.
+# It is not possible to set placement for custom kraken
+# and centrifuge columns.
 
 table_columns_placement:
   FastQC / Falco (pre-Trimming):

diff --git a/conf/modules.config b/conf/modules.config
@@ -181,6 +181,34 @@ process {
         ]
     }
 
+    // Redundancy estimation with nonpareil
+    withName: NONPAREIL_NONPAREIL {
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
+    }
+
+    withName: 'NONPAREIL_CURVE' {
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.png'
+        ]
+    }
+
+    withName: 'NONPAREIL_SET' {
+        ext.prefix = { "nonpareil_all_samples_mqc" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.png'
+        ]
+    }
+
     // AdapterRemoval separate output merging
     withName: CAT_FASTQ {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }

diff --git a/conf/test.config b/conf/test.config
@@ -20,34 +20,35 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
-    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
-    perform_shortread_qc                  = true
-    perform_longread_qc                   = true
-    shortread_qc_mergepairs               = true
-    perform_shortread_complexityfilter    = true
-    perform_shortread_hostremoval         = true
-    perform_longread_hostremoval          = true
-    perform_runmerging                    = true
-    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
-    run_kaiju                             = true
-    run_kraken2                           = true
-    run_bracken                           = true
-    run_malt                              = false
-    run_metaphlan                         = true
-    run_centrifuge                        = true
-    run_diamond                           = true
-    run_krakenuniq                        = true
-    run_motus                             = false
-    run_ganon                             = true
-    run_krona                             = true
-    run_kmcp                              = true
-    kmcp_mode                             = 0
-    krona_taxonomy_directory              = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
-    malt_save_reads                       = true
-    kraken2_save_reads                    = true
-    centrifuge_save_reads                 = true
-    run_profile_standardisation           = true
+    input                                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                              = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
+    perform_shortread_qc                   = true
+    perform_longread_qc                    = true
+    shortread_qc_mergepairs                = true
+    perform_shortread_redundancyestimation = true
+    perform_shortread_complexityfilter     = true
+    perform_shortread_hostremoval          = true
+    perform_longread_hostremoval           = true
+    perform_runmerging                     = true
+    hostremoval_reference                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                              = true
+    run_kraken2                            = true
+    run_bracken                            = true
+    run_malt                               = false
+    run_metaphlan                          = true
+    run_centrifuge                         = true
+    run_diamond                            = true
+    run_krakenuniq                         = true
+    run_motus                              = false
+    run_ganon                              = true
+    run_krona                              = true
+    run_kmcp                               = true
+    kmcp_mode                              = 0
+    krona_taxonomy_directory               = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
+    malt_save_reads                        = true
+    kraken2_save_reads                     = true
+    centrifuge_save_reads                  = true
+    run_profile_standardisation            = true
 }
 
 process {
@@ -61,4 +62,7 @@ process {
     withName: MEGAN_RMA2INFO_KRONA {
         maxForks = 1
     }
+    withName: NONPAREIL_NONPAREIL {
+        ext.args = { "-k 5" }
+    }
 }
diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config
@@ -20,33 +20,37 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
-    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
-    perform_shortread_qc                  = true
-    perform_longread_qc                   = true
-    shortread_qc_tool                     = 'adapterremoval'
-    perform_shortread_complexityfilter    = true
-    perform_shortread_hostremoval         = true
-    perform_longread_hostremoval          = true
-    perform_runmerging                    = true
-    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
-    run_kaiju                             = true
-    run_kraken2                           = true
-    run_bracken                           = false
-    run_malt                              = false
-    run_metaphlan                         = false
-    run_centrifuge                        = false
-    run_diamond                           = false
-    run_krakenuniq                        = false
-    run_motus                             = false
-    run_ganon                             = false
-    run_kmcp                              = false
-    kmcp_mode                             = 0
+    input                                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                              = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
+    perform_shortread_qc                   = true
+    perform_longread_qc                    = true
+    shortread_qc_tool                      = 'adapterremoval'
+    perform_shortread_redundancyestimation = true
+    perform_shortread_complexityfilter     = true
+    perform_shortread_hostremoval          = true
+    perform_longread_hostremoval           = true
+    perform_runmerging                     = true
+    hostremoval_reference                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                              = true
+    run_kraken2                            = true
+    run_bracken                            = false
+    run_malt                               = false
+    run_metaphlan                          = false
+    run_centrifuge                         = false
+    run_diamond                            = false
+    run_krakenuniq                         = false
+    run_motus                              = false
+    run_ganon                              = false
+    run_kmcp                               = false
+    kmcp_mode                              = 0
 }
 
 process {
     withName: MALT_RUN {
         maxForks = 1
         ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
+    withName: NONPAREIL_NONPAREIL {
+        ext.args = { "-k 5" }
+    }
 }
diff --git a/conf/test_bbduk.config b/conf/test_bbduk.config
@@ -49,4 +49,7 @@ process {
         maxForks = 1
         ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
+    withName: NONPAREIL_NONPAREIL {
+        ext.args = { "-k 5" }
+    }
 }
diff --git a/conf/test_falco.config b/conf/test_falco.config
@@ -49,4 +49,7 @@ process {
         maxForks = 1
         ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
+    withName: NONPAREIL_NONPAREIL {
+        ext.args = { "-k 5" }
+    }
 }
diff --git a/conf/test_fastp.config b/conf/test_fastp.config
@@ -20,34 +20,38 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
-    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
-    perform_shortread_qc                  = true
-    perform_longread_qc                   = true
-    shortread_qc_tool                     = 'fastp'
-    perform_shortread_complexityfilter    = true
-    shortread_complexityfilter_tool       = 'fastp'
-    perform_shortread_hostremoval         = true
-    perform_longread_hostremoval          = true
-    perform_runmerging                    = true
-    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
-    run_kaiju                             = true
-    run_kraken2                           = true
-    run_bracken                           = false
-    run_malt                              = false
-    run_metaphlan                         = false
-    run_centrifuge                        = false
-    run_diamond                           = false
-    run_krakenuniq                        = false
-    run_motus                             = false
-    run_ganon                             = false
-    run_kmcp                              = false
-    kmcp_mode                             = 0
+    input                                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                              = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_v1.1.csv'
+    perform_shortread_qc                   = true
+    perform_longread_qc                    = true
+    shortread_qc_tool                      = 'fastp'
+    perform_shortread_redundancyestimation = true
+    perform_shortread_complexityfilter     = true
+    shortread_complexityfilter_tool        = 'fastp'
+    perform_shortread_hostremoval          = true
+    perform_longread_hostremoval           = true
+    perform_runmerging                     = true
+    hostremoval_reference                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                              = true
+    run_kraken2                            = true
+    run_bracken                            = false
+    run_malt                               = false
+    run_metaphlan                          = false
+    run_centrifuge                         = false
+    run_diamond                            = false
+    run_krakenuniq                         = false
+    run_motus                              = false
+    run_ganon                              = false
+    run_kmcp                               = false
+    kmcp_mode                              = 0
 }
 
 process {
     withName: MALT_RUN {
         maxForks = 1
         ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
     }
+    withName: NONPAREIL_NONPAREIL {
+        ext.args = { "-k 5" }
+    }
 }