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integrated dev changes
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@lpantano
lpantano committed Jul 15, 2024
1 parent 36a67a0 commit cc5ca5d
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Showing 6 changed files with 42 additions and 171 deletions.
6 changes: 1 addition & 5 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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}" : ''
Expand Down Expand Up @@ -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}",
Expand Down
128 changes: 38 additions & 90 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand All @@ -111,10 +77,8 @@
},
"gffread": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
Expand All @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -193,10 +147,8 @@
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"installed_by": [
"modules"
]
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
Expand All @@ -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"]
}
}
},
Expand Down
1 change: 1 addition & 0 deletions modules/local/bedtools_genomecov.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ process BEDTOOLS_GENOMECOV {
-ibam $bam \\
-bg \\
-scale \$SCALE_FACTOR \\
$pe \\
$args \\
> tmp.bg
Expand Down
35 changes: 0 additions & 35 deletions modules/nf-core/bedtools/bamtobed/main.nf
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This file was deleted.

38 changes: 0 additions & 38 deletions modules/nf-core/bedtools/bamtobed/meta.yml
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This file was deleted.

5 changes: 2 additions & 3 deletions workflows/atacseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand All @@ -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'
Expand Down

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