Commit 9b5bd8a9 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Added code for new version of samtools view

parent 20237f6c

modules/local/samtools_custom_view.nf

+2 −2
Original line number Diff line number Diff line
@@ -12,9 +12,9 @@ process SAMTOOLS_CUSTOMVIEW { 


    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)

    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

        container "https://depot.galaxyproject.org/singularity/samtools:1.14--h9402c20_2"

        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"

    } else {

        container "quay.io/biocontainers/samtools:1.14--h9402c20_2"

        container "quay.io/biocontainers/samtools:1.14--hb421002_0"

    }



    input:

subworkflows/nf-core/samtools_view_sort_stats.nf

+1 −1
Original line number Diff line number Diff line
@@ -20,7 +20,7 @@ workflow SAMTOOLS_VIEW_SORT_STATS { 
    /*

     * Filter BAM file

     */

    SAMTOOLS_VIEW ( bam )

    SAMTOOLS_VIEW ( bam, [] )

    ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions)



    /*

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