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.github/workflows/ci.yml

@@ -23,7 +23,8 @@ jobs:
           - "21.10.3"
           - "latest-everything"
         parameters:
-          - "--perform_fastqc_alternative false"
+          - "--preprocessing_qc_tool fastqc"
+          - "--preprocessing_qc_tool falco"
           - "--perform_longread_qc false"
           - "--perform_shortread_qc false"
           - "--shortread_qc_tool fastp"

CITATIONS.md

@@ -62,7 +62,7 @@
 
 - [FILTLONG](https://github.com/rrwick/Filtlong)
 
-- [Falco](https://doi.org/10.12688/f1000research.21142.2)
+- [falco](https://doi.org/10.12688/f1000research.21142.2)
 
 > de Sena Brandine G and Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 2021, 8:1874
 

README.md

@@ -30,7 +30,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ![](docs/images/taxprofiler_tube.png)
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`Falco`](https://github.com/smithlabcode/falco) as an alternative option)
+1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`falco`](https://github.com/smithlabcode/falco) as an alternative option)
 2. Performs optional read pre-processing
    - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop))
    - 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))

nextflow.config

@@ -59,6 +59,8 @@ params {
     // Databases
     databases = null
 
+    preprocessing_qc_tool            = 'fastqc'
+
     // FASTQ preprocessing
     perform_shortread_qc             = false
     shortread_qc_tool                = 'fastp'

nextflow_schema.json

@@ -10,7 +10,11 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir", "databases"],
+            "required": [
+                "input",
+                "outdir",
+                "databases"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -80,7 +84,10 @@
                 "shortread_qc_tool": {
                     "type": "string",
                     "default": "fastp",
-                    "enum": ["fastp", "adapterremoval"],
+                    "enum": [
+                        "fastp",
+                        "adapterremoval"
+                    ],
                     "fa_icon": "fas fa-tools",
                     "description": "Specify which tool to use for short-read QC"
                 },
@@ -133,7 +140,11 @@
                 "shortread_complexityfilter_tool": {
                     "type": "string",
                     "default": "bbduk",
-                    "enum": ["bbduk", "prinseqplusplus", "fastp"],
+                    "enum": [
+                        "bbduk",
+                        "prinseqplusplus",
+                        "fastp"
+                    ],
                     "fa_icon": "fas fa-hammer",
                     "description": "Specify which tool to use for complexity filtering"
                 },
@@ -167,7 +178,10 @@
                 "shortread_complexityfilter_prinseqplusplus_mode": {
                     "type": "string",
                     "default": "entropy",
-                    "enum": ["entropy", "dust"],
+                    "enum": [
+                        "entropy",
+                        "dust"
+                    ],
                     "fa_icon": "fas fa-check-square",
                     "description": "Specify the complexity filter mode for PRINSEQ++"
                 },
@@ -341,7 +355,15 @@
                 "diamond_output_format": {
                     "type": "string",
                     "default": "tsv",
-                    "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
+                    "enum": [
+                        "blast",
+                        "xml",
+                        "txt",
+                        "daa",
+                        "sam",
+                        "tsv",
+                        "paf"
+                    ],
                     "fa_icon": "fas fa-file",
                     "description": "Specify output format from DIAMOND profiling.",
                     "help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`"
@@ -360,7 +382,14 @@
                 "kaiju_taxon_rank": {
                     "type": "string",
                     "default": "species",
-                    "enum": ["phylum", "class", "order", "family", "genus", "species"],
+                    "enum": [
+                        "phylum",
+                        "class",
+                        "order",
+                        "family",
+                        "genus",
+                        "species"
+                    ],
                     "fa_icon": "fas fa-tag",
                     "description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
                     "help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`"
@@ -555,7 +584,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -707,5 +743,15 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         }
+    ],
+    "properties": {
+        "preprocessing_qc_tool": {
+            "type": "string",
+            "default": "fastqc",
+            "enum": [
+                "fastqc",
+                "falco"
             ]
+        }
+    }
 }

subworkflows/local/longread_preprocessing.nf

@@ -54,13 +54,13 @@ workflow LONGREAD_PREPROCESSING {
         ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
     }
 
-    if (params.perform_fastqc_alternative) {
+    if (params.preprocessing_qc_tool == 'fastqc') {
-        FALCO_PROCESSED ( ch_processed_reads )
-        ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
-
-    } else {
         FASTQC_PROCESSED ( ch_processed_reads )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
+
+    } else if (params.preprocessing_qc_tool == 'falco') {
+        FALCO_PROCESSED ( ch_processed_reads )
+        ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
     }
 
     emit:

subworkflows/local/shortread_preprocessing.nf

@@ -28,15 +28,14 @@ workflow SHORTREAD_PREPROCESSING {
         ch_processed_reads = reads
     }
 
-    if (params.perform_fastqc_alternative) {
+    if (params.preprocessing_qc_tool == 'fastqc') {
-        FALCO_PROCESSED ( ch_processed_reads )
-        ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
-        ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
-
-    } else {
         FASTQC_PROCESSED ( ch_processed_reads )
         ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
         ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
+    } else if  (params.preprocessing_qc_tool == 'falco') {
+        FALCO_PROCESSED ( ch_processed_reads )
+        ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
+        ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
     }
 
     emit:

workflows/taxprofiler.nf

@@ -121,7 +121,7 @@ workflow TAXPROFILER {
     */
     ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
 
-    if ( params.perform_fastqc_alternative ) {
+    if ( params.preprocessing_qc_tool == 'falco' ) {
         FALCO ( ch_input_for_fastqc )
         ch_versions = ch_versions.mix(FALCO.out.versions.first())
     } else {
@@ -257,9 +257,12 @@ workflow TAXPROFILER {
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
 
-    if (!params.perform_fastqc_alternative) {
+    if (!params.preprocessing_qc_tool == 'falco') {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
     }
+    else {
+        ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect{it[1]}.ifEmpty([]))
+    }
 
     if (params.perform_shortread_qc) {
         ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )