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JoseEspinosaJoseEspinosa
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Patch chromap/chromap module to include read group (otherwise picard/markduplicates erroring)
1 parent cc2b13e commit b209c18

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4 files changed

+196
-47
lines changed

4 files changed

+196
-47
lines changed

‎conf/modules.config

+1
Original file line numberDiff line numberDiff line change
@@ -262,6 +262,7 @@ if (params.aligner == 'chromap') {
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withName: CHROMAP_CHROMAP {
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ext.args = '-l 2000 --low-mem --SAM'
265+
ext.args3 = { meta.read_group ? "-r ${meta.read_group}" : '' }
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ext.prefix = { "${meta.id}.Lb" }
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publishDir = [
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path: { "${params.outdir}/${params.aligner}/library" },

‎modules.json

+149-45
Original file line numberDiff line numberDiff line change
@@ -8,172 +8,253 @@
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"bowtie2/align": {
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"branch": "master",
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"git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
11-
"installed_by": ["fastq_align_bowtie2", "modules"]
11+
"installed_by": [
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"fastq_align_bowtie2",
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"modules"
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]
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},
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"bowtie2/build": {
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"branch": "master",
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"git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bwa/index": {
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"branch": "master",
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"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bwa/mem": {
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"branch": "master",
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"git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
26-
"installed_by": ["fastq_align_bwa", "modules"]
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"installed_by": [
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"fastq_align_bwa",
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"modules"
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]
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},
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"chromap/chromap": {
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"branch": "master",
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"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
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"installed_by": ["fastq_align_chromap", "modules"]
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"installed_by": [
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"fastq_align_chromap",
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"modules"
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],
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"patch": "modules/nf-core/chromap/chromap/chromap-chromap.diff"
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},
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"chromap/index": {
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"branch": "master",
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"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"custom/getchromsizes": {
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"branch": "master",
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"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"deeptools/computematrix": {
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"branch": "master",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"deeptools/plotfingerprint": {
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"branch": "master",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"deeptools/plotheatmap": {
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"branch": "master",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"deeptools/plotprofile": {
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"branch": "master",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
61-
"installed_by": ["modules"]
85+
"installed_by": [
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"modules"
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]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
66-
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
92+
"installed_by": [
93+
"fastq_fastqc_umitools_trimgalore",
94+
"modules"
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]
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},
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"gffread": {
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"branch": "master",
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"git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
71-
"installed_by": ["modules"]
100+
"installed_by": [
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"modules"
102+
]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
76-
"installed_by": ["modules"]
107+
"installed_by": [
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"modules"
109+
]
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},
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"homer/annotatepeaks": {
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"branch": "master",
80113
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
81-
"installed_by": ["modules"]
114+
"installed_by": [
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"modules"
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]
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},
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"khmer/uniquekmers": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
86-
"installed_by": ["modules"]
121+
"installed_by": [
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"modules"
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]
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},
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"macs3/callpeak": {
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"branch": "master",
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"git_sha": "3a3f471ed42f640115b2661edee5b258e6a254c1",
91-
"installed_by": ["modules"]
128+
"installed_by": [
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"modules"
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]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
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"installed_by": ["modules"]
135+
"installed_by": [
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"modules"
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]
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},
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"phantompeakqualtools": {
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"branch": "master",
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"git_sha": "2dfe9afa90fefc70e320140e5f41287f01f324b0",
101-
"installed_by": ["modules"]
142+
"installed_by": [
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"modules"
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]
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},
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"picard/collectmultiplemetrics": {
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"branch": "master",
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"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
106-
"installed_by": ["modules"]
149+
"installed_by": [
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"modules"
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]
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},
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"picard/markduplicates": {
109154
"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
111-
"installed_by": ["bam_markduplicates_picard", "modules"]
156+
"installed_by": [
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"bam_markduplicates_picard",
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"modules"
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]
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},
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"picard/mergesamfiles": {
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"branch": "master",
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"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
116-
"installed_by": ["modules"]
164+
"installed_by": [
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"modules"
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]
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},
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"preseq/lcextrap": {
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"branch": "master",
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"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
121-
"installed_by": ["modules"]
171+
"installed_by": [
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"modules"
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]
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},
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"samtools/flagstat": {
124176
"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
126-
"installed_by": ["bam_stats_samtools", "modules"]
178+
"installed_by": [
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"bam_stats_samtools",
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"modules"
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]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
131-
"installed_by": ["bam_stats_samtools", "modules"]
186+
"installed_by": [
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"bam_stats_samtools",
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"modules"
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]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
194+
"installed_by": [
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools",
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"modules"
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]
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},
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"samtools/sort": {
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"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
141-
"installed_by": ["bam_sort_stats_samtools", "modules"]
203+
"installed_by": [
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"bam_sort_stats_samtools",
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"modules"
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]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
146-
"installed_by": ["bam_stats_samtools", "modules"]
211+
"installed_by": [
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"bam_stats_samtools",
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"modules"
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]
147215
},
148216
"subread/featurecounts": {
149217
"branch": "master",
150218
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
151-
"installed_by": ["modules"]
219+
"installed_by": [
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"modules"
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]
152222
},
153223
"trimgalore": {
154224
"branch": "master",
155225
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
156-
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
226+
"installed_by": [
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"fastq_fastqc_umitools_trimgalore",
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"modules"
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]
157230
},
158231
"ucsc/bedgraphtobigwig": {
159232
"branch": "master",
160233
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
161-
"installed_by": ["modules"]
234+
"installed_by": [
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"modules"
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]
162237
},
163238
"umitools/extract": {
164239
"branch": "master",
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"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
166-
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
241+
"installed_by": [
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"fastq_fastqc_umitools_trimgalore"
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]
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},
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"untar": {
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"branch": "master",
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"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
171-
"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
172251
},
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"untarfiles": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
176-
"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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}
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}
179260
},
@@ -182,55 +263,78 @@
182263
"bam_markduplicates_picard": {
183264
"branch": "master",
184265
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
185-
"installed_by": ["subworkflows"]
266+
"installed_by": [
267+
"subworkflows"
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]
186269
},
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"bam_sort_stats_samtools": {
188271
"branch": "master",
189272
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
190-
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
273+
"installed_by": [
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"fastq_align_bowtie2",
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"fastq_align_bwa",
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"fastq_align_chromap"
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]
191278
},
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"bam_stats_samtools": {
193280
"branch": "master",
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"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
195-
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
282+
"installed_by": [
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools"
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]
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},
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"fastq_align_bowtie2": {
198288
"branch": "master",
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"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
200-
"installed_by": ["subworkflows"]
290+
"installed_by": [
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"subworkflows"
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]
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},
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"fastq_align_bwa": {
203295
"branch": "master",
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"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
205-
"installed_by": ["subworkflows"]
297+
"installed_by": [
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"subworkflows"
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]
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},
207301
"fastq_align_chromap": {
208302
"branch": "master",
209303
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
210-
"installed_by": ["subworkflows"]
304+
"installed_by": [
305+
"subworkflows"
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]
211307
},
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"fastq_fastqc_umitools_trimgalore": {
213309
"branch": "master",
214310
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
215-
"installed_by": ["subworkflows"]
311+
"installed_by": [
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"subworkflows"
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]
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},
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"utils_nextflow_pipeline": {
218316
"branch": "master",
219317
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
220-
"installed_by": ["subworkflows"]
318+
"installed_by": [
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"subworkflows"
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]
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},
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"utils_nfcore_pipeline": {
223323
"branch": "master",
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"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
225-
"installed_by": ["subworkflows"]
325+
"installed_by": [
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"subworkflows"
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]
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},
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"utils_nfvalidation_plugin": {
228330
"branch": "master",
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"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
230-
"installed_by": ["subworkflows"]
332+
"installed_by": [
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"subworkflows"
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]
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}
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}
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}
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}
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}
236-
}
340+
}

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