Commit 7213517b authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Fixed multiqc issue

parent 1f643373

conf/modules.config

+1 −1
Original line number Diff line number Diff line
@@ -259,7 +259,7 @@ params { 
        }



        "multiqc" {

            args          = ""

            args          = "-v"

            publish_dir   = "04_reporting/multiqc"

        }

modules/local/modules/trimgalore/main.nf

+4 −4
Original line number Diff line number Diff line
@@ -86,11 +86,11 @@ process TRIMGALORE { 
        mv ${meta.id}_1_val_1.fq.gz ${prefix_1}.fastq.gz

        mv ${meta.id}_2_val_2.fq.gz ${prefix_2}.fastq.gz



        [ ! -f  ${meta.id}_1_val_1_fastqc.html ] || mv ${meta.id}_1_val_1_fastqc.html ${meta.id}_1_fastqc${suffix}.html

        [ ! -f  ${meta.id}_2_val_2_fastqc.html ] || mv ${meta.id}_2_val_2_fastqc.html ${meta.id}_2_fastqc${suffix}.html

        [ ! -f  ${meta.id}_1_val_1_fastqc.html ] || mv ${meta.id}_1_val_1_fastqc.html ${meta.id}_1${suffix}_fastqc.html

        [ ! -f  ${meta.id}_2_val_2_fastqc.html ] || mv ${meta.id}_2_val_2_fastqc.html ${meta.id}_2${suffix}_fastqc.html



        [ ! -f  ${meta.id}_1_val_1_fastqc.zip ] || mv ${meta.id}_1_val_1_fastqc.zip ${meta.id}_1_fastqc${suffix}.zip

        [ ! -f  ${meta.id}_2_val_2_fastqc.zip ] || mv ${meta.id}_2_val_2_fastqc.zip ${meta.id}_2_fastqc${suffix}.zip

        [ ! -f  ${meta.id}_1_val_1_fastqc.zip ] || mv ${meta.id}_1_val_1_fastqc.zip ${meta.id}_1${suffix}_fastqc.zip

        [ ! -f  ${meta.id}_2_val_2_fastqc.zip ] || mv ${meta.id}_2_val_2_fastqc.zip ${meta.id}_2${suffix}_fastqc.zip

        """

    }

}

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