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Bulk update of modules and subworkflows for 2.1.0 release #410

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merged 13 commits into from
Aug 9, 2024
Merged

Bulk update of modules and subworkflows for 2.1.0 release #410

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d9d10ac
Update modules and subworkflows
JoseEspinosa Jul 31, 2024
4897569
Update local subworkflow
JoseEspinosa Jul 31, 2024
c3b5edf
Merge remote-tracking branch 'upstream/dev' into updates
JoseEspinosa Jul 31, 2024
beda39a
Update bwa/mem
JoseEspinosa Aug 6, 2024
a3e2814
Update chromap modules
JoseEspinosa Aug 6, 2024
d9e9805
Updating deeptools modules
JoseEspinosa Aug 6, 2024
6de6032
Update modules.json
JoseEspinosa Aug 6, 2024
cc2b13e
Update changelog
JoseEspinosa Aug 6, 2024
b209c18
Patch chromap/chromap module to include read group (otherwise picard/…
JoseEspinosa Aug 7, 2024
fce3e6c
Make lint happy
JoseEspinosa Aug 7, 2024
ab04e58
Update multiqc version
JoseEspinosa Aug 8, 2024
07134ee
Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-chi…
JoseEspinosa Aug 8, 2024
2cc4f57
Update changelog with updated versions
JoseEspinosa Aug 8, 2024
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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.
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maybe a list of which ones were updated would be helpful to figure out where behavior might have changed.

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Good point! I updated the changelog to show the versions updated here


### 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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