Commit 4128c703 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Updated modules

parent 5124619f

modules.json

+8 −8
Original line number Diff line number Diff line
@@ -28,7 +28,7 @@ 
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

            },

            "custom/getchromsizes": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "950700bcdc0e9a2b6883d40d2c51c6fc435cd714"

            },

            "deeptools/computematrix": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -49,22 +49,22 @@ 
                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

            },

            "samtools/flagstat": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"

            },

            "samtools/idxstats": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"

            },

            "samtools/index": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"

            },

            "samtools/sort": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"

            },

            "samtools/stats": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"

            },

            "samtools/view": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"

            },

            "seacr/callpeak": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -76,7 +76,7 @@ 
                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"

            },

            "untar": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

                "git_sha": "7ec09d0ef4df89617baacc9b2dafcddb7cd4b05a"

            }

        }

    }

modules/nf-core/modules/custom/getchromsizes/main.nf

+3 −3
Original line number Diff line number Diff line
@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES { 
    tag "$fasta"

    label 'process_low'



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

    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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

        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"

        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :

        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"



    input:

    path fasta

modules/nf-core/modules/samtools/flagstat/main.nf

+3 −3
Original line number Diff line number Diff line
@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT { 
    tag "$meta.id"

    label 'process_low'



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

    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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

        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"

        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :

        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"



    input:

    tuple val(meta), path(bam), path(bai)

modules/nf-core/modules/samtools/idxstats/main.nf

+3 −3
Original line number Diff line number Diff line
@@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS { 
    tag "$meta.id"

    label 'process_low'



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

    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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

        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"

        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :

        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"



    input:

    tuple val(meta), path(bam), path(bai)

modules/nf-core/modules/samtools/index/main.nf

+3 −3
Original line number Diff line number Diff line
@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { 
    tag "$meta.id"

    label 'process_low'



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

    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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

        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"

        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :

        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"



    input:

    tuple val(meta), path(input)

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