Merge pull request #641 from jfy133/metagenomic-complexity-filter

jfy133 · web-flow · commit 492b1aa7ff03 · 2020-12-23T21:58:50.000+01:00
Add pre-metagenomic screening complexity filter
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -146,16 +146,16 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_pmdtools
       - name: GENOTYPING_UG AND MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
       - name: COMPLEX LANE/LIBRARY MERGING Test running lane and library merging prior to GATK UnifiedGenotyper and running MultiVCFAnalyzer
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
       - name: GENOTYPING_UG ON TRIMMED BAM Test
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
-         nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, convert to FASTQ for adapterremoval test and downstream
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --run_convertinputbam
@@ -167,6 +167,9 @@ jobs:
       - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into MALT
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --malt_sam_output
+      - name: METAGENOMIC Run the basic pipeline but low-complexity filtered reads going into MALT
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --metagenomic_complexity_filter
       - name: MALTEXTRACT Download resource files
         run: |
             mkdir -p databases/maltextract
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-- [#583](https://github.com/nf-core/eager/issues/583) - mapDamage2 rescaling of BAM files to remove damage
+- [#640](https://github.com/nf-core/eager/issues/640) - Added a pre-metagenomic screening filtering of low-sequence complexity reads with `bbduk`
+- [#583](https://github.com/nf-core/eager/issues/583) - Added `mapDamage2` rescaling of BAM files to remove damage
 
 ### `Fixed`
 
diff --git a/README.md b/README.md
@@ -25,7 +25,39 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
     <img src="docs/images/output/overview/eager2_workflow.png" alt="nf-core/eager schematic workflow" width="70%"
 </p>
 
-## Pipeline steps
+## Quick Start
+
+1. Install [`nextflow`](https://nf-co.re/usage/installation) (version >= 20.04.0)
+
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+
+3. Download the pipeline and test it on a minimal dataset with a single command:
+
+    ```bash
+    nextflow run nf-core/eager -profile test,<docker/singularity/podman/conda/institute>
+    ```
+
+    > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+
+4. Start running your own analysis!
+
+    ```bash
+    nextflow run nf-core/eager -profile <docker/singularity/conda> --input '*_R{1,2}.fastq.gz' --fasta '<your_reference>.fasta'
+    ```
+
+5. Once your run has completed successfully, clean up the intermediate files.
+
+    ```bash
+    nextflow clean -f -k
+    ```
+
+See [usage docs](https://nf-co.re/eager/docs/usage.md) for all of the available options when running the pipeline.
+
+**N.B.** You can see an overview of the run in the MultiQC report located at `./results/MultiQC/multiqc_report.html`
+
+Modifications to the default pipeline are easily made using various options as described in the documentation.
+
+## Pipeline Summary
 
 ### Default Steps
 
@@ -77,6 +109,7 @@ Additional functionality contained by the pipeline currently includes:
 
 #### Metagenomic Screening
 
+* Low-sequenced complexity filtering (`BBduk`)
 * Taxonomic binner with alignment (`MALT`)
 * Taxonomic binner without alignment (`Kraken2`)
 * aDNA characteristic screening of taxonomically binned data from MALT (`MaltExtract`)
@@ -89,48 +122,6 @@ A graphical overview of suggested routes through the pipeline depending on conte
     <img src="docs/images/output/overview/eager2_metromap_complex.png" alt="nf-core/eager metro map" width="70%"
 </p>
 
-## Quick Start
-
-1. Install [`nextflow`](https://nf-co.re/usage/installation) (version >= 20.04.0)
-
-2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
-
-3. Download the pipeline and test it on a minimal dataset with a single command:
-
-    ```bash
-    nextflow run nf-core/eager -profile test,<docker/singularity/podman/conda/institute>
-    ```
-
-    > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-
-4. Start running your own analysis!
-
-    ```bash
-    nextflow run nf-core/eager -profile <docker/singularity/conda> --input '*_R{1,2}.fastq.gz' --fasta '<your_reference>.fasta'
-    ```
-
-5. Once your run has completed successfully, clean up the intermediate files.
-
-    ```bash
-    nextflow clean -f -k
-    ```
-
-See [usage docs](https://nf-co.re/eager/docs/usage.md) for all of the available options when running the pipeline.
-
-**N.B.** You can see an overview of the run in the MultiQC report located at `./results/MultiQC/multiqc_report.html`
-
-Modifications to the default pipeline are easily made using various options
-as described in the documentation.
-
-## Pipeline Summary
-
-By default, the pipeline currently performs the following:
-
-<!-- TODO nf-core: Fill in short bullet-pointed list of default steps of pipeline -->
-
-* Sequencing quality control (`FastQC`)
-* Overall pipeline run summaries (`MultiQC`)
-
 ## Documentation
 
 The nf-core/eager pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/eager/usage) and [output](https://nf-co.re/eager/output).
@@ -237,6 +228,7 @@ In addition, references of tools and data used in this pipeline are as follows:
 * **sequenceTools** Stephan Schiffels (Unpublished). Download: [https://github.com/stschiff/sequenceTools](https://github.com/stschiff/sequenceTools)
 * **EigenstratDatabaseTools** Thiseas C. Lamnidis (Unpublished). Download: [https://github.com/TCLamnidis/EigenStratDatabaseTools.git](https://github.com/TCLamnidis/EigenStratDatabaseTools.git)
 * **mapDamage2** Jónsson, H., et al 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics , 29(13), 1682–1684. [https://doi.org/10.1093/bioinformatics/btt193](https://doi.org/10.1093/bioinformatics/btt193)
+* **BBduk** Brian Bushnell (Unpublished). Download: [https://sourceforge.net/projects/bbmap/](sourceforge.net/projects/bbmap/)
 
 ## Data References
 
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -6,7 +6,6 @@ report_comment: >
     This report has been generated by the <a href="https://github.com/nf-core/eager" target="_blank">nf-core/eager</a>
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://github.com/nf-core/eager" target="_blank">documentation</a>.
-
 run_modules:
     - adapterRemoval
     - bowtie2
@@ -270,4 +269,4 @@ report_section_order:
     nf-core-eager-summary:
         order: -1001
 
-export_plots: true
+export_plots: true
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
@@ -37,6 +37,7 @@
     'kraken':['v_kraken.txt', r"Kraken version (\S+)"],
     'eigenstrat_snp_coverage':['v_eigenstrat_snp_coverage.txt',r"(\S+)"],
     'mapDamage2':['v_mapdamage.txt',r"(\S+)"],
+    'bbduk':['v_bbduk.txt',r"(\S+)"]
 }
 
 results = OrderedDict()
@@ -73,6 +74,8 @@
 results['maltextract'] = '<span style="color:#999999;\">N/A</span>'
 results['eigenstrat_snp_coverage'] = '<span style="color:#999999;\">N/A</span>'
 results['mapDamage2'] = '<span style="color:#999999;\">N/A</span>'
+results['bbduk'] = '<span style="color:#999999;\">N/A</span>'
+
 
 # Search each file using its regex
 for k, v in regexes.items():
diff --git a/docs/output.md b/docs/output.md
@@ -664,6 +664,7 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
 - `sex_determination/` - this contains the output for the sex determination run. This is a single `.tsv` file that includes a table with the sample name, the number of autosomal SNPs, number of SNPs on the X/Y chromosome, the number of reads mapping to the autosomes, the number of reads mapping to the X/Y chromosome, the relative coverage on the X/Y chromosomes, and the standard error associated with the relative coverages. These measures are provided for each bam file, one row per file. If the `sexdeterrmine_bedfile` option has not been provided, the error bars cannot be trusted, and runtime will be considerably longer.
 - `nuclear_contamination/` - this contains the output of the nuclear contamination processes. The directory contains one `*.X.contamination.out` file per individual, as well as `nuclear_contamination.txt` which is a summary table of the results for all individual. `nuclear_contamination.txt` contains a header, followed by one line per individual, comprised of the Method of Moments (MOM) and Maximum Likelihood (ML) contamination estimate (with their respective standard errors) for both Method1 and Method2.
 - `bedtools/` - this contains two files as the output from bedtools coverage. One file contains the 'breadth' coverage (`*.breadth.gz`). This file will have the contents of your annotation file (e.g. BED/GFF), and the following subsequent columns: no. reads on feature, # bases at depth, length of feature, and % of feature. The second file (`*.depth.gz`), contains the contents of your annotation file (e.g. BED/GFF), and an additional column which is mean depth coverage (i.e. average number of reads covering each position).
+- `metagenomic_complexity_filter` - this contains the output from filtering of input reads to metagenomic classification of low-sequence complexity reads as performed by `bbduk`. This will include the filtered FASTQ files (`*_lowcomplexityremoved.fq.gz`) and also the run-time log (`_bbduk.stats`) for each sample. **Note:** there are no sections in the MultiQC report for this module, therefore you must check the `._bbduk.stats` files to get summary statistics of the filtering.
 - `metagenomic_classification/` - this contains the output for a given metagenomic classifier.
   - Running MALT will contain RMA6 files that can be loaded into MEGAN6 or MaltExtract for phylogenetic visualisation of read taxonomic assignments and aDNA characteristics respectively. Additional a `malt.log` file is provided which gives additional information such as run-time, memory usage and per-sample statistics of numbers of alignments with taxonomic assignment etc. This will also include gzip SAM files if requested.
   - Running kraken will contain the Kraken output and report files, as well as a merged Taxon count table.
diff --git a/environment.yml b/environment.yml
@@ -48,3 +48,5 @@ dependencies:
   - bioconda::bowtie2=2.4.1
   - bioconda::eigenstratdatabasetools=1.0.2
   - bioconda::mapdamage2=2.2.0
+  - bioconda::bbmap=38.87
+
diff --git a/main.nf b/main.nf
diff --git a/nextflow.config b/nextflow.config
diff --git a/nextflow_schema.json b/nextflow_schema.json
