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Merge pull request #410 from JoseEspinosa/updates
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Bulk update of modules and subworkflows for 2.1.0 release
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@JoseEspinosa
JoseEspinosa committed Aug 9, 2024
2 parents d489e97 + 2cc4f57 commit 686c054
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26 changes: 18 additions & 8 deletions CHANGELOG.md
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Expand Up @@ -30,19 +30,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#378](https://github.com/nf-core/chipseq/issues/378)] - Switch from macs2 to macs3.
- [[#347](https://github.com/nf-core/chipseq/issues/347)] - Add read group tag to bam files processed by bowtie2.
- [[PR #406](https://github.com/nf-core/chipseq/pull/406)] - Update metro map to show macs3 instead of macs2.
- [[#409](https://github.com/nf-core/chipseq/issues/409)] - Bulk modules and subworkflows update.

### Software dependencies

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.

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `chromap` | 0.2.1 | 0.2.4 |
| `macs2` | 2.2.7.1 | |
| `macs3` | | 3.0.1 |
| `multiqc` | 1.13 | 1.14 |
| `picard` | 2.27.4 | 3.0.0 |
| `samtools` | 1.15.1 | 1.17 |
| Dependency | Old version | New version |
| ----------------------- | ----------- | ----------- |
| `bowtie2` | 2.4.4 | 2.5.2 |
| `bwa` | 0.7.17 | 0.7.18 |
| `chromap` | 0.2.1 | 0.2.6 |
| `deeptools` | 3.5.1 | 3.5.5 |
| `fastqc` | 0.11.9 | 0.12.1 |
| `gffread` | 0.12.1 | 0.12.7 |
| `gffread` | 0.12.1 | 0.12.7 |
| `macs2` | 2.2.7.1 | |
| `macs3` | | 3.0.1 |
| `multiqc` | 1.13 | 1.23 |
| `picard` | 2.27.4 | 3.2.0 |
| `samtools` | 1.15.1 | 1.20 |
| `samtools` | 1.15.1 | 1.20 |
| `ucsc-bedgraphtobigwig` | 377 | 445 |
| `umi_tools` | | 1.1.5 |

> **NB:** Dependency has been **updated** if both old and new version information is present.
> **NB:** Dependency has been **added** if just the new version information is present.
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11 changes: 0 additions & 11 deletions assets/multiqc_config.yml
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Expand Up @@ -7,17 +7,6 @@ data_format: "yaml"

export_plots: true

run_modules:
- custom_content
- fastqc
- cutadapt
- samtools
- picard
- preseq
- featureCounts
- deeptools
- phantompeakqualtools

exclude_modules:
- "general_stats"

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1 change: 1 addition & 0 deletions conf/modules.config
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Expand Up @@ -262,6 +262,7 @@ if (params.aligner == 'chromap') {

withName: CHROMAP_CHROMAP {
ext.args = '-l 2000 --low-mem --SAM'
ext.args3 = { meta.read_group ? "-r ${meta.read_group}" : '' }
ext.prefix = { "${meta.id}.Lb" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/library" },
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79 changes: 40 additions & 39 deletions modules.json
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Expand Up @@ -7,82 +7,83 @@
"nf-core": {
"bowtie2/align": {
"branch": "master",
"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
"git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
"installed_by": ["fastq_align_bowtie2", "modules"]
},
"bowtie2/build": {
"branch": "master",
"git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
"git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d",
"installed_by": ["modules"]
},
"bwa/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
"installed_by": ["modules"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
"installed_by": ["fastq_align_bwa", "modules"]
},
"chromap/chromap": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["fastq_align_chromap", "modules"]
"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
"installed_by": ["fastq_align_chromap", "modules"],
"patch": "modules/nf-core/chromap/chromap/chromap-chromap.diff"
},
"chromap/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["modules"]
},
"deeptools/computematrix": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"deeptools/plotfingerprint": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"deeptools/plotheatmap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"deeptools/plotprofile": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"gffread": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
},
"homer/annotatepeaks": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"khmer/uniquekmers": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"macs3/callpeak": {
Expand All @@ -92,7 +93,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
"installed_by": ["modules"]
},
"phantompeakqualtools": {
Expand All @@ -102,77 +103,77 @@
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_markduplicates_picard", "modules"]
},
"picard/mergesamfiles": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
"installed_by": ["modules"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools", "modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"untar": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
},
"untarfiles": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
}
}
Expand All @@ -181,27 +182,27 @@
"nf-core": {
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
},
"fastq_align_bowtie2": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["subworkflows"]
},
"fastq_align_bwa": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
"installed_by": ["subworkflows"]
},
"fastq_align_chromap": {
Expand All @@ -211,7 +212,7 @@
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
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6 changes: 3 additions & 3 deletions modules/local/multiqc.nf
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@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_medium'

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

input:
path workflow_summary
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28 changes: 23 additions & 5 deletions modules/nf-core/bowtie2/align/main.nf
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