Issue 162 add assembler qc report

.gitignore

@@ -10,3 +10,4 @@ testing*
 .screenrc
 eggnog
 kofam/
+eukulele/

CITATIONS.md

@@ -45,7 +45,7 @@
 
 - [Prodigal](https://github.com/hyattpd/Prodigal)
 
-- [BBmap] (https://sourceforge.net/projects/bbmap/)
+- [BBmap](https://sourceforge.net/projects/bbmap/)
 
 - [FeatureCounts](https://subread.sourceforge.net)
 
@@ -73,8 +73,13 @@
 - [EUKulele](https://github.com/AlexanderLabWHOI/EUKulele)
 
 - [CAT](https://github.com/dutilh/CAT)
+
   > von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biology. 2019;20:217.
 
+- [transrate](https://hibberdlab.com/transrate/)
+
+  > TransRate: reference free quality assessment of de-novo transcriptome assemblies (2016). Richard D Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, Steven Kelly. Genome Research doi: [http://dx.doi.org/10.1101/gr.196469.115](http://dx.doi.org/10.1101/gr.196469.115)
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

assets/multiqc_config.yml

@@ -11,3 +11,17 @@ report_section_order:
     order: -1002
 
 export_plots: true
+
+custom_data:
+  megahit_assemblies:
+    description: "Describes assembly statistics, generated by TransRate."
+    plot_type: table
+  rnaspades_assemblies:
+    description: "Describes assembly statistics, generated by TransRate."
+    plot_type: table
+
+custom_plot_config:
+  megahit_assemblies-plot:
+    col1_header: "File Name"
+  rnaspades_assemblies-plot:
+    col1_header: "File Name"

modules/local/transrate.nf

@@ -0,0 +1,41 @@
+process TRANSRATE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::transrate=1.0.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/transrate:1.0.3--hec16e2b_4':
+        'biocontainers/transrate:1.0.3--hec16e2b_4' }"
+
+    input:
+    tuple val(meta), path(assembly)
+
+    output:
+    tuple val(meta), path("*assemblies_mqc.csv") , emit: assembly_qc
+    path "versions.yml"                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+
+    transrate \\
+        --threads $task.cpus \\
+        --assembly $assembly \\
+        --output ${prefix}_transrate \\
+        $args
+
+    mv ${prefix}_transrate/assemblies.csv ${prefix}_assemblies_mqc.csv
+
+    # transrate flashes a warning about a ruby gem being out of date, so call the version before it is being piped into the yaml
+    transrate --version > version.txt
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        transrate: \$(cat version.txt)
+    END_VERSIONS
+    """
+}

workflows/metatdenovo.nf

@@ -112,6 +112,7 @@ include { FORMATSPADES                     } from '../modules/local/formatspades
 include { UNPIGZ as UNPIGZ_CONTIGS         } from '../modules/local/unpigz'
 include { UNPIGZ as UNPIGZ_GFF             } from '../modules/local/unpigz'
 include { MERGE_TABLES                     } from '../modules/local/merge_summary_tables'
+include { TRANSRATE                        } from '../modules/local/transrate'
 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
@@ -385,7 +386,7 @@ workflow METATDENOVO {
     BAM_SORT_STATS_SAMTOOLS ( BBMAP_ALIGN.out.bam, ch_assembly_contigs )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
-    // if ( orf_caller == 
+    // if ( orf_caller ==
     BAM_SORT_STATS_SAMTOOLS.out.bam
         .combine(ch_gff.map { it[1] } )
         .set { ch_featurecounts }
@@ -448,6 +449,12 @@ workflow METATDENOVO {
             .set { ch_merge_tables }
 
     }
+
+    // set up contig channel to use in CAT and TransRate
+    UNPIGZ_CONTIGS(ch_assembly_contigs)
+    ch_unzipped_contigs = UNPIGZ_CONTIGS.out.unzipped
+    ch_versions = ch_versions.mix(UNPIGZ_CONTIGS.out.versions)
+
     //
     // CAT: Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins)
     //
@@ -460,9 +467,8 @@ workflow METATDENOVO {
             CAT_DB_GENERATE ()
             ch_cat_db = CAT_DB_GENERATE.out.db
         }
-        UNPIGZ_CONTIGS(ch_assembly_contigs)
         CAT_CONTIGS (
-            UNPIGZ_CONTIGS.out.unzipped,
+            ch_unzipped_contigs,
             ch_cat_db
         )
         CAT_SUMMARY(
@@ -472,6 +478,12 @@ workflow METATDENOVO {
         ch_versions = ch_versions.mix(CAT_SUMMARY.out.versions)
     }
 
+    //
+    // MODULE: Use TransRate to judge assembly quality, piped into MultiQC
+    //
+    TRANSRATE(ch_unzipped_contigs)
+    ch_versions = ch_versions.mix(TRANSRATE.out.versions)
+
     //
     // SUBWORKFLOW: Eukulele
     //
@@ -526,6 +538,7 @@ workflow METATDENOVO {
 
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(TRANSRATE.out.assembly_qc.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(BAM_SORT_STATS_SAMTOOLS.out.idxstats.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(FEATURECOUNTS_CDS.out.summary.collect{it[1]}.ifEmpty([]))