clean up

nf-core · Sep 17, 2024 · 1514ea7 · 1514ea7
1 parent 7922b5f
commit 1514ea7
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diff --git a/conf/modules.config b/conf/modules.config
@@ -19,10 +19,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-<<<<<<< HEAD
-    withName: FASTQC {
-        ext.args = '--quiet'
-=======
     // nanoseq.nf includes
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
@@ -61,24 +57,15 @@ if (!params.skip_demultiplexing) {
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
->>>>>>> origin/add_dorado
     }
 }
 
-<<<<<<< HEAD
-    withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-=======
 if (params.run_nanolyse) {
     withName: GET_NANOLYSE_FASTA {
         publishDir = [
             path: { "${params.outdir}/nanolyse" },
             mode: 'copy',
             enabled: false,
->>>>>>> origin/add_dorado
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }

diff --git a/workflows/nanoseq.nf b/workflows/nanoseq.nf
@@ -152,7 +152,6 @@ include { QCAT                        } from '../modules/nf-core/qcat/main'
 include { NANOLYSE                    } from '../modules/nf-core/nanolyse/main'
 include { CUSTOM_GETCHROMSIZES        } from '../modules/nf-core/custom/getchromsizes/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
->>>>>>> origin/add_dorado
 
 /*
  * SUBWORKFLOW: Consisting entirely of nf-core/modules
@@ -168,80 +167,6 @@ include { QUANTIFY_STRINGTIE_FEATURECOUNTS } from '../subworkflows/local/quantif
 /* --           RUN MAIN WORKFLOW              -- */
 ////////////////////////////////////////////////////
 
-<<<<<<< HEAD
-workflow NANOSEQ {
-
-    take:
-    ch_samplesheet // channel: samplesheet read in from --input
-
-    main:
-
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
-
-    //
-    // MODULE: Run FastQC
-    //
-    FASTQC (
-        ch_samplesheet
-    )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
-
-    //
-    // Collate and save software versions
-    //
-    softwareVersionsToYAML(ch_versions)
-        .collectFile(
-            storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
-            sort: true,
-            newLine: true
-        ).set { ch_collated_versions }
-
-    //
-    // MODULE: MultiQC
-    //
-    ch_multiqc_config        = Channel.fromPath(
-        "$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()
-
-    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_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)
-    ch_multiqc_files = ch_multiqc_files.mix(
-        ch_methods_description.collectFile(
-            name: 'methods_description_mqc.yaml',
-            sort: true
-        )
-    )
-
-    MULTIQC (
-        ch_multiqc_files.collect(),
-        ch_multiqc_config.toList(),
-        ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
-    )
-
-    emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
-    versions       = ch_versions                 // channel: [ path(versions.yml) ]
-=======
 // Info required for completion email and summary
 def multiqc_report      = []