Commit 6300d7d6 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Merge branch 'chris-feat' into v2.0

parents fb403f62 1ec9c629

.github/workflows/ci.yml

+6 −0
Original line number Diff line number Diff line
@@ -163,6 +163,12 @@ jobs: 
          - verify_output_align_duplicates_remove

          - verify_output_align_duplicates_remove_target

          - verify_output_peak_calling_only_peak_calling

          - test_bam_scale_none

          - test_bam_scale_spikein

          - test_bam_scale_cpm

          - test_bam_scale_rpkm

          - test_bam_scale_bpm

          - test_bam_scale_cpm_iggscale

          - test_peak_callers

          - test_conseneus_peaks_group

          - test_conseneus_peaks_all

conf/modules.config

+2 −2
Original line number Diff line number Diff line
@@ -170,7 +170,7 @@ if(params.run_trim_galore_fastqc && !params.skip_trimming) { 
if(params.run_alignment) {

    process {

        withName: '.*:ALIGN_BOWTIE2:BOWTIE2_ALIGN' {

            ext.args   = '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700'

            ext.args   = { params.skip_trimming ? '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700' : '--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700' }

            publishDir = [

                [

                    path: { "${params.outdir}/02_alignment/${params.aligner}/target/log" },
@@ -193,7 +193,7 @@ if(params.run_alignment) { 
        }



        withName: '.*:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN' {

            ext.args   = '--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700'

            ext.args   = { params.skip_trimming ? '--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700' : '--local --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700' }

            ext.prefix = { "${meta.id}.spikein" }

            publishDir = [

                [

modules.json

+0 −3
Original line number Diff line number Diff line
@@ -30,9 +30,6 @@ 
            "custom/getchromsizes": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

            },

            "deeptools/bamcoverage": {

                "git_sha": "fdb1664885480d9411c24ba45bb4fde4738e5907"

            },

            "deeptools/computematrix": {

                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

            },

modules/nf-core/modules/deeptools/bamcoverage/main.nf→modules/local/modules/deeptools/bamcoverage/main.nf

+2 −1
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ process DEEPTOOLS_BAMCOVERAGE { 
        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"



    input:

    tuple val(meta), path(input), path(input_index)

    tuple val(meta), path(input), path(input_index), val(scale)



    output:

    tuple val(meta), path("*.bigWig")   , emit: bigwig, optional: true
@@ -26,6 +26,7 @@ process DEEPTOOLS_BAMCOVERAGE { 
    bamCoverage \

    --bam $input \

    $args \

    --scaleFactor ${scale} \

    --numberOfProcessors ${task.cpus} \

    --outFileName ${prefix}

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