Commit b626be2c authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Switched to biocontainer mulled for reporting

parent af9e4ca5

modules/local/modules/calculate_frip/main.nf

+3 −1
Original line number Diff line number Diff line
@@ -3,7 +3,9 @@ process CALCULATE_FRIP { 
    label 'process_low'



    conda (params.enable_conda ? "conda-forge::python=3.8.3 bioconda::deeptools=3.5.* bioconda::pysam=0.17.*" : null)

    container "chrischeshire/nfcore-cutandrun:latest"

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

        'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' :

        'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"



    input:

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

modules/local/modules/calculate_peak_reprod/main.nf

+3 −1
Original line number Diff line number Diff line
@@ -3,7 +3,9 @@ process CALCULATE_PEAK_REPROD { 
    label 'process_ultralow'



    conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::dask=2021.9.1 conda-forge::pandas=1.3.3" : null)

    container "chrischeshire/nfcore-cutandrun:latest"

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

        'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' :

        'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"



    input:

    tuple val(meta), path(bed)

modules/local/modules/generate_reports/main.nf

+3 −1
Original line number Diff line number Diff line
@@ -2,7 +2,9 @@ process GENERATE_REPORTS { 
    label 'process_ultralow'



    conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::pandas=1.3.3" : null)

    container "chrischeshire/nfcore-cutandrun:latest"

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

        'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' :

        'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"



    input:

    path meta_data

modules/local/modules/plot_consensus_peaks/main.nf

+3 −1
Original line number Diff line number Diff line
@@ -2,7 +2,9 @@ process PLOT_CONSENSUS_PEAKS { 
    label 'process_min'



    conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4" : null)

    container "chrischeshire/nfcore-cutandrun:latest"

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

        'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' :

        'quay.io/biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }"



    input:

    path(consensus_peaks)

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