Update syntax + add workflow output definitions

conf/modules.config

@@ -12,12 +12,6 @@
 
 process {
 
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-
     // BWA MEM
     withName: "BWA_MEM" {
         ext.args = {[
@@ -33,7 +27,6 @@ process {
 
     // Picard CrosscheckFingerprints
     withName: "PICARD_CROSSCHECKFINGERPRINTS" {
-        publishDir = [ enabled:false ]
         ext.args = {[
             "--CROSSCHECK_BY SAMPLE",
             "--CROSSCHECK_MODE CHECK_ALL_OTHERS",
@@ -47,7 +40,6 @@ process {
     }
 
     withName: "NGSBITS_SAMPLEGENDER" {
-        publishDir = [ enabled:false ]
         ext.prefix = { "${meta.id}.xy" }
         ext.args   = "-max_female ${params.max_yx_female} -min_male ${params.min_yx_male}"
         ext.args2  = "-min_female ${params.min_hetx_female} -max_male ${params.max_hetx_male}"
@@ -56,20 +48,10 @@ process {
 
     withName: 'MULTIQC_POOLS' {
         ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}_${meta.id}\"" : "--title \"$meta.id\"" }
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
     withName: 'MULTIQC_MAIN' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
     }
 
 }

main.nf

@@ -17,41 +17,6 @@ include { SAMPLETRACKING  } from './workflows/sampletracking'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_sampletracking_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_sampletracking_pipeline'
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOWS FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-//
-// WORKFLOW: Run main analysis pipeline depending on type of input
-//
-workflow NFCMGG_SAMPLETRACKING {
-
-    take:
-    samplesheet // channel: samplesheet read in from --input
-    bwa_index   // channel: bwa index file
-    genome_fasta // channel: genome fasta file
-    haplotype_map // channel: haplotype map file
-    outdir       // channel: output directory
-
-    main:
-
-    //
-    // WORKFLOW: Run pipeline
-    //
-    SAMPLETRACKING (
-        samplesheet,
-        bwa_index,
-        genome_fasta,
-        haplotype_map,
-        outdir
-    )
-    emit:
-    multiqc_report = SAMPLETRACKING.out.multiqc_report // channel: /path/to/multiqc_report.html
-}
-/*
-
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     RUN MAIN WORKFLOW
@@ -67,7 +32,6 @@ workflow {
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
-        params.monochrome_logs,
         args,
         params.outdir,
         params.input,
@@ -79,22 +43,25 @@ workflow {
     //
     // WORKFLOW: Run main workflow
     //
-    NFCMGG_SAMPLETRACKING (
+    SAMPLETRACKING (
         PIPELINE_INITIALISATION.out.samplesheet,
-        Channel.value([
+        channel.value([
             [id: "bwa"],
             file(params.bwa_index, checkIfExists: true)
         ]),
-        Channel.value(
+        channel.value(
             [[id:"genome_fasta"],
             file(params.fasta, checkIfExists: true),
             file(params.fai, checkIfExists: true),
         ]),
-        Channel.value(
+        channel.value(
             [[id:"haplotype_map"],
             file(params.haplotype_map, checkIfExists: true)
         ]),
-        params.outdir
+        params.outdir,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description
     )
     //
     // SUBWORKFLOW: Run completion tasks
@@ -106,8 +73,17 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        NFCMGG_SAMPLETRACKING.out.multiqc_report
+        SAMPLETRACKING.out.multiqc_report
     )
+
+    publish:
+    multiqc_report = SAMPLETRACKING.out.multiqc_report
+    multiqc_pools  = SAMPLETRACKING.out.multiqc_pools
+}
+
+output {
+    multiqc_report { path "multiqc/" }
+    multiqc_pools  { path "multiqc/" }
 }
 
 /*

modules.json

@@ -29,7 +29,7 @@
                     },
                     "picard/crosscheckfingerprints": {
                         "branch": "master",
-                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
+                        "git_sha": "4e8415483e3119fc3035ece12ec9236dac261357",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/picard/crosscheckfingerprints/picard-crosscheckfingerprints.diff"
                     },
@@ -49,7 +49,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

nextflow.config

@@ -283,3 +283,6 @@ validation {
     defaultIgnoreParams = []
     monochromeLogs = params.monochrome_logs
 }
+
+workflow.output.mode = params.publish_dir_mode
+outputDir = params.outdir

subworkflows/local/utils_nfcore_sampletracking_pipeline/main.nf

@@ -29,7 +29,6 @@ workflow PIPELINE_INITIALISATION {
     take:
     version           // boolean: Display version and exit
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
-    monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
     input             //  string: Path to input samplesheet
@@ -39,7 +38,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -89,7 +88,7 @@ workflow PIPELINE_INITIALISATION {
             return counts
         })
 
-    Channel
+    channel
         .fromList(input_list)
         .map {
             meta, sample_bam, sample_bam_index, snp_fastq_1, snp_fastq_2, snp_bam, snp_bam_index ->

workflows/sampletracking.nf

@@ -39,9 +39,9 @@ workflow SAMPLETRACKING {
 
     main:
 
-    def ch_versions = Channel.empty()
-    def ch_multiqc_files = Channel.empty()
-    def ch_pool_multiqc_files = Channel.empty()
+    def ch_versions = channel.empty()
+    def ch_multiqc_files = channel.empty()
+    def ch_pool_multiqc_files = channel.empty()
 
 
     def (ch_sample, ch_snp, ch_rest) = ch_samplesheet
@@ -109,7 +109,7 @@ workflow SAMPLETRACKING {
     // Crosscheck fingerprints
     //
 
-    def ch_crosscheck_metrics_out = Channel.empty()
+    def ch_crosscheck_metrics_out = channel.empty()
     ch_samplesheet_fixed
         .filter { meta, _sample_bam, _sample_bam_index, snp_fastq, snp_bam, _snp_bam_index ->
             if(!snp_bam && !snp_fastq) {
@@ -169,7 +169,7 @@ workflow SAMPLETRACKING {
     //
     // Determine sample sex
     //
-    def ch_sex_prediction_out = Channel.empty()
+    def ch_sex_prediction_out = channel.empty()
     ch_samplesheet_fixed
         .map { meta, sample_bam, sample_bam_index, _snp_fastq, _snp_bam, _snp_bam_index ->
             [ meta, sample_bam, sample_bam_index ]
@@ -267,24 +267,24 @@ workflow SAMPLETRACKING {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
+    ch_multiqc_config        = channel.fromPath(
         "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_custom_config = multiqc_config ?
-        Channel.fromPath(multiqc_config, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(multiqc_config, checkIfExists: true) :
+        channel.empty()
     ch_multiqc_logo          = multiqc_logo ?
-        Channel.fromPath(multiqc_logo, checkIfExists: true) :
-        Channel.empty()
+        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_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_custom_methods_description = multiqc_methods_description ?
         file(multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
+    ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)