Unverified Commit 810edea7 authored by Chris Cheshire's avatar Chris Cheshire Committed by GitHub
Browse files

Merge pull request #82 from luslab/dev 

Small release changes
parents e0aed056 530d7382

modules/local/linux/awk.nf

+1 −1
Original line number Original line Diff line number Diff line
@@ -13,7 +13,7 @@ process AWK { 
        mode: params.publish_dir_mode,

        mode: params.publish_dir_mode,

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }





    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)

    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)

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

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

        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"

        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"

    } else {

    } else {

modules/local/linux/awk_script.nf

+1 −1
Original line number Original line Diff line number Diff line
@@ -11,7 +11,7 @@ process AWK_SCRIPT { 
        mode: params.publish_dir_mode,

        mode: params.publish_dir_mode,

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }





    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)

    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)

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

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

        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"

        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"

    } else {

    } else {

workflows/cutandrun.nf

+2 −1
Original line number Original line Diff line number Diff line
@@ -880,6 +880,7 @@ workflow CUTANDRUN { 
                ch_seacr_bed.collect{it[1]}.ifEmpty([]),

                ch_seacr_bed.collect{it[1]}.ifEmpty([]),

                UCSC_BEDGRAPHTOBIGWIG.out.bigwig.collect{it[1]}.ifEmpty([])

                UCSC_BEDGRAPHTOBIGWIG.out.bigwig.collect{it[1]}.ifEmpty([])

            )

            )

            //TODO - this version ouptut causes an error for an unknown reason

            //ch_software_versions = ch_software_versions.mix(IGV_SESSION.out.versions)

            //ch_software_versions = ch_software_versions.mix(IGV_SESSION.out.versions)

        }

        }

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