Multiqc metrics

CHANGELOG.md

@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.2.0dev
 
+### New features
+
+1. The metrics are now in the multiqc report instead of in a separate file
+
 ### Changes
 
 1. Updated the pipeline template to nf-core v2.13.1

main.nf

@@ -20,6 +20,24 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_wise
 params.fasta = getGenomeAttribute('fasta')
 params.fai   = getGenomeAttribute('fai')
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    ADDITIONAL INPUT VALIDATION
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+def List val_bin_sizes = params.bin_sizes.split(",").collect { it as Integer }
+def Integer lowestBinSize = val_bin_sizes.min()
+val_bin_sizes.each { bin_size ->
+    if(bin_size % lowestBinSize != 0) {
+        error("""
+All bin sizes should be divisible by the lowest bin size! 
+${bin_size} is not divisible by ${lowestBinSize}...
+""")
+    }
+}
+
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -53,7 +71,16 @@ workflow NFCMGG_WISECONDORX {
     // WORKFLOW: Run pipeline
     //
     WISECONDORX (
-        samplesheet
+        samplesheet,
+        params.fasta,
+        params.fai,
+        val_bin_sizes,
+        params.no_metrics,
+        params.prefix,
+        params.outdir,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
     )
 
     emit:

tests/main.nf.test

@@ -13,7 +13,7 @@ nextflow_pipeline {
                 input  = "${projectDir}/tests/inputs/samplesheet.csv"
                 outdir = "${outputDir}"
                 prefix = "test_reference"
-                bin_sizes = "10000,5"
+                bin_sizes = "10,5"
                 max_cpus   = 2
                 max_memory = '6.GB'
                 max_time   = '6.h'

tests/main.nf.test.snap

@@ -5,7 +5,6 @@
 
             ],
             [
-                "metrics.txt:md5,bdb678960431c256e283e21d6e1db1ed",
                 [
                     [
 
@@ -14,7 +13,7 @@
                     "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "test_reference_10kbp.npz:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_reference_5bp.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "test_reference_5kbp.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {

workflows/wisecondorx.nf

@@ -24,7 +24,16 @@ include { methodsDescriptionText      } from '../subworkflows/local/utils_nfcore
 workflow WISECONDORX {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
+    ch_samplesheet              // queue channel:   samplesheet read in from --input
+    fasta                       // string:          the reference fasta file
+    fai                         // string:          the index of the reference fasta file
+    val_bin_sizes               // list:            a list of bin sizes to use
+    no_metrics                  // boolean:         deactivate the generation of metrics
+    prefix                      // string:          the prefix to be used by the output file
+    outdir                      // string:          the path of the output directory
+    multiqc_config              // string:          the path to the multiqc config
+    multiqc_logo                // string:          the path to the multiqc logo
+    multiqc_methods_description // file:            the file containing the multiqc custom method descriptions
 
     main:
 
@@ -35,11 +44,11 @@ workflow WISECONDORX {
     // Create optional input files
     //
 
-    ch_fasta = Channel.fromPath(params.fasta, checkIfExists:true)
-        .map { [[id:params.genome ?: "fasta"], it] }
+    ch_fasta = Channel.fromPath(fasta, checkIfExists:true)
+        .map { [[id:"fasta"], it] }
         .collect()
 
-    if(!params.fai) {
+    if(!fai) {
         SAMTOOLS_FAIDX(
             ch_fasta,
             [[],[]]
@@ -49,8 +58,8 @@ workflow WISECONDORX {
         SAMTOOLS_FAIDX.out.fai
             .set { ch_fai }
     } else {
-        ch_fai = Channel.fromPath(params.fai, checkIfExists:true)
-            .map { [[id:params.genome ?: "fasta"], it] }
+        ch_fai = Channel.fromPath(fai, checkIfExists:true)
+            .map { [[id:"fasta"], it] }
             .collect()
     }
 
@@ -76,7 +85,7 @@ workflow WISECONDORX {
         .mix(ch_input.indexed)
         .set { ch_indexed }
 
-    if(!params.no_metrics){
+    if(!no_metrics){
 
         //
         // Define the gender if it's not given
@@ -119,6 +128,10 @@ workflow WISECONDORX {
                 counts
             }
             .map { genders -> create_metrics(genders)}
+            .collectFile(name: "metrics_mqc.tsv")
+            .set { ch_metrics }
+
+        ch_multiqc_files = ch_multiqc_files.mix(ch_metrics)
 
     }
 
@@ -143,11 +156,11 @@ workflow WISECONDORX {
 
     WISECONDORX_CONVERT.out.npz
         .map { meta, npz ->
-            new_meta = [id:params.prefix ?: dateFormat]
+            new_meta = [id:prefix ?: dateFormat]
             [ new_meta, npz ]
         }
         .groupTuple() // All files should be present here, so no size is needed
-        .combine(params.bin_sizes.split(","))
+        .combine(val_bin_sizes)
         .map { meta, npz, bin_size ->
             new_meta = meta + [bin_size:bin_size]
             [ new_meta, npz ]
@@ -161,18 +174,18 @@ workflow WISECONDORX {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
+        .collectFile(storeDir: "${outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
         .set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
     ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+    ch_multiqc_custom_config              = multiqc_config ? Channel.fromPath(multiqc_config, checkIfExists: true) : Channel.empty()
+    ch_multiqc_logo                       = multiqc_logo ? Channel.fromPath(multiqc_logo, checkIfExists: true) : Channel.empty()
     summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_multiqc_custom_methods_description = multiqc_methods_description
     ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
@@ -202,20 +215,17 @@ def get_gender(tsv) {
 }
 
 def create_metrics(genders) {
-    male = genders["male"]
-    female = genders["female"]
-    male_count = male.size()
-    female_count = female.size()
-    total_count = male_count + female_count
-    ratio_male_to_female = male_count / female_count
-
-    output = file("${params.outdir}/metrics.txt")
-    output.write("Ratio male to female: ${ratio_male_to_female}\n")
-    output.append("Male count: ${male_count}\n")
-    output.append("Female count: ${female_count}\n")
-    output.append("Total count: ${total_count}\n")
-    output.append("Males: ${male.join(',')}\n")
-    output.append("Females: ${female.join(',')}\n")
+    def List male = genders["male"]
+    def List female = genders["female"]
+    def Integer male_count = male.size()
+    def Integer female_count = female.size()
+    def Float male_to_female_ratio = male_count / female_count
+    def Integer total_count = male_count + female_count
+
+    return """# plot_type: 'table'
+Male to female ratio\tMale count\tFemale count\tTotal count\tMales\tFemales
+${male_to_female_ratio}\t${male_count}\t${female_count}\t${total_count}\t${male.join(",")}\t${female.join(",")}
+"""
 }
 
 /*