Commit 2f7e4997 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Macs2 will now use the igenomes genome parameter

parent a4ccca9d

nextflow.config

+1 −1
Original line number Diff line number Diff line
@@ -72,7 +72,7 @@ params { 


    // MACS2 Peak Calling

    macs2_pvalue               = 0.05

    macs2_gsize                = 2.7e9

    macs_gsize                = 2.7e9

    run_narrow_peak            = false



    // Consensus Peaks

nextflow_schema.json

+2 −2
Original line number Diff line number Diff line
@@ -344,11 +344,11 @@ 
                    "fa_icon": "fas fa-align-justify",

                    "description": "P-value threshold for macs2 peak caller"

                },

                "macs2_gsize": {

                "macs_gsize": {

                    "type": "number",

                    "default": 2700000000.0,

                    "fa_icon": "fas fa-align-justify",

                    "description": "Genome size values for macs2 peak caller"

                    "description": "parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize will default to GRCh38."

                },

                "run_narrow_peak": {

                    "type": "boolean",

workflows/cutandrun.nf

+2 −2
Original line number Diff line number Diff line
@@ -487,7 +487,7 @@ workflow CUTANDRUN { 


                MACS2_CALLPEAK (

                    ch_bam_paired,

                    params.macs2_gsize

                    params.macs_gsize

                )

                ch_macs2_bed         = MACS2_CALLPEAK.out.bed

                ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK.out.versions)
@@ -536,7 +536,7 @@ workflow CUTANDRUN { 


                MACS2_CALLPEAK_NOIGG (

                    ch_samtools_bam_target_fctrl,

                    params.macs2_gsize

                    params.macs_gsize

                )

                ch_macs2_bed         = MACS2_CALLPEAK_NOIGG.out.bed

                ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK_NOIGG.out.versions)

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