diff --git a/conf/modules.config b/conf/modules.config index c913b0c4..9fa07d5d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -615,12 +615,9 @@ if (!params.skip_plot_fingerprint) { process { withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:MACS2_CALLPEAK' { ext.args = [ - '--format BED', '--keep-dup all', '--nomodel', - '--shift -75', - '--extsize 150', - params.narrow_peak ? '--call-summits' : "--broad --broad-cutoff ${params.broad_cutoff}", + params.narrow_peak ? '' : "--broad --broad-cutoff ${params.broad_cutoff}", params.save_macs_pileup ? '--bdg --SPMR' : '', params.macs_pvalue ? "--pvalue ${params.macs_pvalue}" : '', params.macs_fdr ? "--qvalue ${params.macs_fdr}" : '' @@ -875,7 +872,6 @@ if (!params.skip_merge_replicates) { process { withName: '.*:MERGED_REPLICATE_CALL_ANNOTATE_PEAKS:MACS2_CALLPEAK' { ext.args = [ - '--format BED', '--keep-dup all', '--nomodel', params.narrow_peak ? '' : "--broad --broad-cutoff ${params.broad_cutoff}", diff --git a/modules.json b/modules.json index 5f6bbeb1..8a987a57 100644 --- a/modules.json +++ b/modules.json @@ -7,24 +7,13 @@ "nf-core": { "ataqv/ataqv": { "branch": "master", - "git_sha": "56421e1a812bc2f9e77dbe9f297e9d9c580cb8a5", - "installed_by": [ - "modules" - ] + "git_sha": "11c7e5b3073845889060c793786bf3177275d62e", + "installed_by": ["modules"] }, "ataqv/mkarv": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] - }, - "bedtools/bamtobed": { - "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "git_sha": "11c7e5b3073845889060c793786bf3177275d62e", + "installed_by": ["modules"] }, "bowtie2/align": { "branch": "master", @@ -33,17 +22,13 @@ }, "bowtie2/build": { "branch": "master", - "git_sha": "e797efb47b0d3b2124753beb55dc83ab9512bceb", - "installed_by": [ - "modules" - ] + "git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c", + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", - "git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", @@ -57,52 +42,33 @@ }, "chromap/index": { "branch": "master", - "git_sha": "3a8e3ca607132a468c07c69aaa3bccd55eb983b8", - "installed_by": [ - "modules" - ] - }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "deeptools/computematrix": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "deeptools/plotfingerprint": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "deeptools/plotheatmap": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "deeptools/plotprofile": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "fastqc": { "branch": "master", @@ -111,10 +77,8 @@ }, "gffread": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "gunzip": { "branch": "master", @@ -128,24 +92,18 @@ }, "khmer/uniquekmers": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "macs2/callpeak": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", @@ -154,17 +112,13 @@ }, "picard/mergesamfiles": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "preseq/lcextrap": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", @@ -193,10 +147,8 @@ }, "subread/featurecounts": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", @@ -210,17 +162,13 @@ }, "umitools/extract": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "fastq_fastqc_umitools_trimgalore" - ] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "untar": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", - "installed_by": [ - "modules" - ] + "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "installed_by": ["modules"] } } }, diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf index d286abf8..2b751b90 100644 --- a/modules/local/bedtools_genomecov.nf +++ b/modules/local/bedtools_genomecov.nf @@ -33,6 +33,7 @@ process BEDTOOLS_GENOMECOV { -ibam $bam \\ -bg \\ -scale \$SCALE_FACTOR \\ + $pe \\ $args \\ > tmp.bg diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf deleted file mode 100644 index 29f5a62f..00000000 --- a/modules/nf-core/bedtools/bamtobed/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -process BEDTOOLS_BAMTOBED { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::bedtools=2.30.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'biocontainers/bedtools:2.30.0--hc088bd4_0' }" - - input: - tuple val(meta), path(bam) - - output: - tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - bedtools \\ - bamtobed \\ - $args \\ - -i $bam \\ - > ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - END_VERSIONS - """ -} diff --git a/modules/nf-core/bedtools/bamtobed/meta.yml b/modules/nf-core/bedtools/bamtobed/meta.yml deleted file mode 100644 index 5a4ff73a..00000000 --- a/modules/nf-core/bedtools/bamtobed/meta.yml +++ /dev/null @@ -1,38 +0,0 @@ -name: bedtools_bamtobed -description: Converts a bam file to a bed12 file. -keywords: - - bam - - bed -tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html - licence: ["MIT"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed file containing genomic intervals. - pattern: "*.{bed}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@yuukiiwa" - - "@drpatelh" diff --git a/workflows/atacseq.nf b/workflows/atacseq.nf index 9e9dca64..2ca2c026 100644 --- a/workflows/atacseq.nf +++ b/workflows/atacseq.nf @@ -17,8 +17,8 @@ include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_atacseq_pipeline' -include { INPUT_CHECK } from '../subworkflows/local/input_check' -include { ALIGN_STAR } from '../subworkflows/local/align_star' +include { INPUT_CHECK } from '../subworkflows/local/input_check' +include { ALIGN_STAR } from '../subworkflows/local/align_star' include { BAM_SHIFT_READS as MERGED_LIBRARY_BAM_SHIFT_READS } from '../subworkflows/local/bam_shift_reads' include { BAM_SHIFT_READS as MERGED_REPLICATE_BAM_SHIFT_READS } from '../subworkflows/local/bam_shift_reads' include { BIGWIG_PLOT_DEEPTOOLS as MERGED_LIBRARY_BIGWIG_PLOT_DEEPTOOLS } from '../subworkflows/local/bigwig_plot_deeptools' @@ -45,7 +45,6 @@ include { PRESEQ_LCEXTRAP as MERGED_LIBRARY_PRESEQ_LCEXTRAP include { DEEPTOOLS_PLOTFINGERPRINT as MERGED_LIBRARY_DEEPTOOLS_PLOTFINGERPRINT } from '../modules/nf-core/deeptools/plotfingerprint/main' include { ATAQV_ATAQV as MERGED_LIBRARY_ATAQV_ATAQV } from '../modules/nf-core/ataqv/ataqv/main' include { ATAQV_MKARV as MERGED_LIBRARY_ATAQV_MKARV } from '../modules/nf-core/ataqv/mkarv/main' -include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main' include { PICARD_MERGESAMFILES as PICARD_MERGESAMFILES_LIBRARY } from '../modules/nf-core/picard/mergesamfiles/main' include { PICARD_MERGESAMFILES as PICARD_MERGESAMFILES_REPLICATE } from '../modules/nf-core/picard/mergesamfiles/main'