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Revert "Revert "DO NOT MERGE yet: Discuss fixes of #164 #168 #169 ""
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This reverts commit 1030a66.
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@lpantano
lpantano committed Jul 12, 2024
1 parent 30a165a commit 7d31e7f
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Showing 11 changed files with 430 additions and 58 deletions.
68 changes: 67 additions & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -457,6 +457,37 @@ process {
]
}

withName: '.*:MERGED_LIBRARY_BAM_SHIFT_READS:DEEPTOOLS_ALIGNMENTSIEVE' {
ext.args = '--ATACshift'
ext.prefix = { "${meta.id}.mLb.clN.shifted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/shifted_reads" },
mode: params.publish_dir_mode,
pattern: '*.bam',
enabled: params.save_align_intermeds
]
}

withName: '.*:MERGED_LIBRARY_BAM_SHIFT_READS:SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}.mLb.clN.shifted.sorted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/shifted_reads" },
mode: params.publish_dir_mode,
pattern: '*.bam',
enabled: params.shift_reads
]
}

withName: '.*:MERGED_LIBRARY_BAM_SHIFT_READS:SAMTOOLS_INDEX' {
ext.prefix = { "${meta.id}.mLb.clN.shifted.sorted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/shifted_reads" },
mode: params.publish_dir_mode,
pattern: '*.bai',
enabled: params.shift_reads
]
}

withName: '.*:MERGED_LIBRARY_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV' {
ext.args = { (meta.single_end && params.fragment_size > 0) ? "-fs ${params.fragment_size}" : '' }
ext.prefix = { "${meta.id}.mLb.clN" }
Expand Down Expand Up @@ -584,9 +615,12 @@ if (!params.skip_plot_fingerprint) {
process {
withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:MACS2_CALLPEAK' {
ext.args = [
'--format BED',
'--keep-dup all',
'--nomodel',
params.narrow_peak ? '' : "--broad --broad-cutoff ${params.broad_cutoff}",
'--shift -75',
'--extsize 150',
params.narrow_peak ? '--call-summits' : "--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}" : ''
Expand Down Expand Up @@ -778,6 +812,37 @@ if (!params.skip_merge_replicates) {
]
}

withName: '.*:MERGED_REPLICATE_BAM_SHIFT_READS:DEEPTOOLS_ALIGNMENTSIEVE' {
ext.args = '--ATACshift'
ext.prefix = { "${meta.id}.mRp.clN.shifted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate" },
mode: params.publish_dir_mode,
pattern: '*.bam',
enabled: params.save_align_intermeds
]
}

withName: '.*:MERGED_REPLICATE_BAM_SHIFT_READS:SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}.mRp.clN.shifted.sorted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/shifted_reads" },
mode: params.publish_dir_mode,
pattern: '*.bam',
enabled: params.shift_reads
]
}

withName: '.*:MERGED_REPLICATE_BAM_SHIFT_READS:SAMTOOLS_INDEX' {
ext.prefix = { "${meta.id}.mRp.clN.shifted.sorted" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/shifted_reads" },
mode: params.publish_dir_mode,
pattern: '*.bai',
enabled: params.shift_reads
]
}

withName: '.*:MERGED_REPLICATE_BAM_TO_BIGWIG:BEDTOOLS_GENOMECOV' {
ext.args = { (meta.single_end && params.fragment_size > 0) ? "-fs ${params.fragment_size}" : '' }
ext.prefix = { "${meta.id}.mRp.clN" }
Expand Down Expand Up @@ -810,6 +875,7 @@ 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}",
Expand Down
128 changes: 90 additions & 38 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,24 @@
"nf-core": {
"ataqv/ataqv": {
"branch": "master",
"git_sha": "11c7e5b3073845889060c793786bf3177275d62e",
"installed_by": ["modules"]
"git_sha": "56421e1a812bc2f9e77dbe9f297e9d9c580cb8a5",
"installed_by": [
"modules"
]
},
"ataqv/mkarv": {
"branch": "master",
"git_sha": "11c7e5b3073845889060c793786bf3177275d62e",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"bedtools/bamtobed": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
},
"bowtie2/align": {
"branch": "master",
Expand All @@ -22,13 +33,17 @@
},
"bowtie2/build": {
"branch": "master",
"git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
"installed_by": ["modules"]
"git_sha": "e797efb47b0d3b2124753beb55dc83ab9512bceb",
"installed_by": [
"modules"
]
},
"bwa/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65",
"installed_by": [
"modules"
]
},
"bwa/mem": {
"branch": "master",
Expand All @@ -42,33 +57,52 @@
},
"chromap/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "3a8e3ca607132a468c07c69aaa3bccd55eb983b8",
"installed_by": [
"modules"
]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
"installed_by": [
"modules"
]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
"installed_by": [
"modules"
]
},
"deeptools/computematrix": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"deeptools/plotfingerprint": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"deeptools/plotheatmap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"deeptools/plotprofile": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"fastqc": {
"branch": "master",
Expand All @@ -77,8 +111,10 @@
},
"gffread": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"gunzip": {
"branch": "master",
Expand All @@ -92,18 +128,24 @@
},
"khmer/uniquekmers": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"macs2/callpeak": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"picard/markduplicates": {
"branch": "master",
Expand All @@ -112,13 +154,17 @@
},
"picard/mergesamfiles": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"samtools/flagstat": {
"branch": "master",
Expand Down Expand Up @@ -147,8 +193,10 @@
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
},
"trimgalore": {
"branch": "master",
Expand All @@ -162,13 +210,17 @@
},
"umitools/extract": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"fastq_fastqc_umitools_trimgalore"
]
},
"untar": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
}
}
},
Expand Down
1 change: 0 additions & 1 deletion modules/local/bedtools_genomecov.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@ process BEDTOOLS_GENOMECOV {
-ibam $bam \\
-bg \\
-scale \$SCALE_FACTOR \\
$pe \\
$args \\
> tmp.bg
Expand Down
36 changes: 36 additions & 0 deletions modules/local/deeptools_alignmentsieve.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
process DEEPTOOLS_ALIGNMENTSIEVE {
tag "$meta.id"
label 'process_medium'

conda "bioconda::deeptools=3.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' :
'biocontainers/deeptools:3.5.1--py_0' }"

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

output:
tuple val(meta), path("*.bam"), emit: bam
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}"

"""
alignmentSieve \\
$args \\
-b $bam \\
-o ${prefix}.bam \\
--numberOfProcessors $task.cpus
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeptools: \$(alignmentSieve --version | sed -e "s/alignmentSieve //g")
END_VERSIONS
"""
}
35 changes: 35 additions & 0 deletions modules/nf-core/bedtools/bamtobed/main.nf
View file

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