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Merge pull request #410 from JoseEspinosa/updates
Bulk update of modules and subworkflows for 2.1.0 release
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‎CHANGELOG.md‎

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@@ -30,19 +30,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- [[#378](https://github.com/nf-core/chipseq/issues/378)] - Switch from macs2 to macs3.
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- [[#347](https://github.com/nf-core/chipseq/issues/347)] - Add read group tag to bam files processed by bowtie2.
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- [[PR #406](https://github.com/nf-core/chipseq/pull/406)] - Update metro map to show macs3 instead of macs2.
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- [[#409](https://github.com/nf-core/chipseq/issues/409)] - Bulk modules and subworkflows update.
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### Software dependencies
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Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `chromap` | 0.2.1 | 0.2.4 |
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| `macs2` | 2.2.7.1 | |
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| `macs3` | | 3.0.1 |
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| `multiqc` | 1.13 | 1.14 |
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| `picard` | 2.27.4 | 3.0.0 |
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| `samtools` | 1.15.1 | 1.17 |
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| Dependency | Old version | New version |
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| ----------------------- | ----------- | ----------- |
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| `bowtie2` | 2.4.4 | 2.5.2 |
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| `bwa` | 0.7.17 | 0.7.18 |
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| `chromap` | 0.2.1 | 0.2.6 |
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| `deeptools` | 3.5.1 | 3.5.5 |
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| `fastqc` | 0.11.9 | 0.12.1 |
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| `gffread` | 0.12.1 | 0.12.7 |
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| `gffread` | 0.12.1 | 0.12.7 |
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| `macs2` | 2.2.7.1 | |
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| `macs3` | | 3.0.1 |
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| `multiqc` | 1.13 | 1.23 |
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| `picard` | 2.27.4 | 3.2.0 |
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| `samtools` | 1.15.1 | 1.20 |
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| `samtools` | 1.15.1 | 1.20 |
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| `ucsc-bedgraphtobigwig` | 377 | 445 |
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| `umi_tools` | | 1.1.5 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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> **NB:** Dependency has been **added** if just the new version information is present.

‎assets/multiqc_config.yml‎

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export_plots: true
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run_modules:
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- custom_content
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- fastqc
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- cutadapt
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- samtools
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- picard
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- preseq
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- featureCounts
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- deeptools
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- phantompeakqualtools
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exclude_modules:
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- "general_stats"
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‎conf/modules.config‎

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withName: CHROMAP_CHROMAP {
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ext.args = '-l 2000 --low-mem --SAM'
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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

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"nf-core": {
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"bowtie2/align": {
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"branch": "master",
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"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
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"git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
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"installed_by": ["fastq_align_bowtie2", "modules"]
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},
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"bowtie2/build": {
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"branch": "master",
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"git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
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"git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d",
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"installed_by": ["modules"]
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},
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"bwa/index": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
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"installed_by": ["modules"]
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},
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"bwa/mem": {
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"branch": "master",
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
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"installed_by": ["fastq_align_bwa", "modules"]
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},
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"chromap/chromap": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"installed_by": ["fastq_align_chromap", "modules"]
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"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
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"installed_by": ["fastq_align_chromap", "modules"],
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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": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
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"installed_by": ["modules"]
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},
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"custom/getchromsizes": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
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"installed_by": ["modules"]
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},
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"deeptools/computematrix": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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},
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"deeptools/plotfingerprint": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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},
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"deeptools/plotheatmap": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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},
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"deeptools/plotprofile": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
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"installed_by": ["modules"]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
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},
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"gffread": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
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"installed_by": ["modules"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
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"installed_by": ["modules"]
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},
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"homer/annotatepeaks": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"installed_by": ["modules"]
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},
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"khmer/uniquekmers": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"installed_by": ["modules"]
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},
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"macs3/callpeak": {
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
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"git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
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"installed_by": ["modules"]
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},
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"phantompeakqualtools": {
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},
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"picard/collectmultiplemetrics": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
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"installed_by": ["modules"]
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},
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"picard/markduplicates": {
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"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_markduplicates_picard", "modules"]
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},
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"picard/mergesamfiles": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
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"installed_by": ["modules"]
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},
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"preseq/lcextrap": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
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"installed_by": ["modules"]
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_stats_samtools", "modules"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_stats_samtools", "modules"]
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},
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"samtools/index": {
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
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},
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"samtools/sort": {
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"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"samtools/stats": {
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"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["bam_stats_samtools", "modules"]
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"subread/featurecounts": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
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},
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"trimgalore": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
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"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
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},
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"ucsc/bedgraphtobigwig": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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},
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"umitools/extract": {
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"branch": "master",
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"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
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"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
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"installed_by": ["fastq_fastqc_umitools_trimgalore"]
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},
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"untar": {
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"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
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"untarfiles": {
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"branch": "master",
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"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"installed_by": ["modules"]
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"nf-core": {
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"bam_markduplicates_picard": {
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"branch": "master",
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"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["subworkflows"]
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},
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"bam_sort_stats_samtools": {
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"branch": "master",
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"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
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"bam_stats_samtools": {
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"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
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"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
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"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
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"fastq_align_bowtie2": {
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"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
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"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
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"fastq_align_bwa": {
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"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
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"fastq_align_chromap": {
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"fastq_fastqc_umitools_trimgalore": {
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"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
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"utils_nextflow_pipeline": {

‎modules/local/multiqc.nf‎

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conda "bioconda::multiqc=1.13a"
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conda "bioconda::multiqc=1.23"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1':
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'biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
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'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' :
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'biocontainers/multiqc:1.23--pyhdfd78af_0' }"
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path workflow_summary

‎modules/nf-core/bowtie2/align/main.nf‎

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