Commit 3940babb authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Changed all yaml to yml

parent 8f1f5657

modules/local/modules/generate_reports/main.nf

+2 −2
Original line number Diff line number Diff line
@@ -18,7 +18,7 @@ process GENERATE_REPORTS { 
    path '*.pdf'             , emit: pdf

    path '*.csv'             , emit: csv

    path '*.png'             , emit: png

    path '*frag_len_mqc.yaml', emit: frag_len_multiqc

    path '*frag_len_mqc.yml', emit: frag_len_multiqc

    path  "versions.yml"     , emit: versions



    when:
@@ -38,7 +38,7 @@ process GENERATE_REPORTS { 
        --log log.txt



    if [ -f "03_03_frag_len_mqc.txt" ]; then

        cat $frag_len_header_multiqc 03_03_frag_len_mqc.txt > frag_len_mqc.yaml

        cat $frag_len_header_multiqc 03_03_frag_len_mqc.txt > frag_len_mqc.yml

    fi



    cat <<-END_VERSIONS > versions.yml

workflows/cutandrun.nf

+2 −2
Original line number Diff line number Diff line
@@ -55,7 +55,7 @@ ch_dt_frag_to_csv_awk = file("$projectDir/bin/dt_frag_report_to_csv.awk", checkI 
*/



// Load up and check multiqc base config and custom configs

ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)

ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)

ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()



// Header files for MultiQC
@@ -952,7 +952,7 @@ workflow CUTANDRUN { 
            ch_multiqc_custom_config.collect().ifEmpty([]),

            CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),

            CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_unique_yml.collect(),

            ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml"),

            ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yml"),

            FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]),

            FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]),

            FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]),

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