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Update FastQC and UMItools modules #1138

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merged 9 commits into from
Dec 8, 2023
Merged

Update FastQC and UMItools modules #1138

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277af7d
Update FastQC and UMItools modules
mahesh-panchal Dec 8, 2023
d6803dc
Update CHANGELOG
mahesh-panchal Dec 8, 2023
8fed9ff
Merge branch 'dev' into dev
maxulysse Dec 8, 2023
8e66ae3
Update modules with stderr updated
mahesh-panchal Dec 8, 2023
c9fd01c
Update Changelog
mahesh-panchal Dec 8, 2023
9e5cdc7
Fix formatting
mahesh-panchal Dec 8, 2023
75dde11
Update channel names from bam_rseqc subworkflow update
mahesh-panchal Dec 8, 2023
a294bb5
Update bam_rseqc subworkflow again
mahesh-panchal Dec 8, 2023
ed2b8aa
Update CHANGELOG.md
mahesh-panchal Dec 8, 2023
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15 changes: 15 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,11 +10,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Enhancements & fixes

- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling.
- [PR #1138](https://github.com/nf-core/rnaseq/pull/1138) - Updates FASTQC and UMITOOLS modules and their dependencies which have had their version string extraction commands updated ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
- Update Rseqc and Fastp modules to print STDERR to screen and file.

### Software dependencies

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| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `picard` | 3.0.0 | 3.1.1 |
| `samtools` | 1.17 | 1.18 |

> **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.
>
> **NB:** Dependency has been **removed** if new version information isn't present.

### Modules / Subworkflows

- BAM_RSEQC subworkflow updated with new channel names.

## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21

### Credits
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64 changes: 32 additions & 32 deletions modules.json
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Expand Up @@ -27,12 +27,12 @@
},
"fastp": {
"branch": "master",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
"installed_by": ["modules", "fastq_fastqc_umitools_fastp"]
},
"fastqc": {
"branch": "master",
"git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
},
"fq/subsample": {
Expand Down Expand Up @@ -77,7 +77,7 @@
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
"git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
"installed_by": ["bam_markduplicates_picard"]
},
"preseq/lcextrap": {
Expand All @@ -102,42 +102,42 @@
},
"rseqc/bamstat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "65acf692457e8c466e104c6a3e5ac392e98fe688",
"installed_by": ["bam_rseqc"]
},
"rseqc/inferexperiment": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f2a3328fde9a2b4185285057f8d3727f39dd2aef",
"installed_by": ["bam_rseqc"]
},
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"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "3e839096a1be5da4f68d1de1066e4d0bc13f5d6d",
"installed_by": ["bam_rseqc"]
},
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"installed_by": ["bam_rseqc"]
},
"rseqc/readdistribution": {
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"installed_by": ["bam_rseqc"]
},
"rseqc/readduplication": {
"branch": "master",
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"installed_by": ["bam_rseqc"]
},
"rseqc/tin": {
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "4acfdd20843d5b6d63f9181721a6856447cb7bec",
"installed_by": ["bam_rseqc"]
},
"salmon/index": {
Expand All @@ -152,31 +152,31 @@
},
"samtools/flagstat": {
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"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": ["bam_stats_samtools"]
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"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": [
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
"bam_sort_stats_samtools",
"bam_dedup_stats_samtools_umitools"
"bam_sort_stats_samtools"
]
},
"samtools/sort": {
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"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
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"installed_by": ["bam_stats_samtools"]
},
"sortmerna": {
Expand Down Expand Up @@ -206,7 +206,7 @@
},
"trimgalore": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"ucsc/bedclip": {
Expand All @@ -221,13 +221,13 @@
},
"umitools/dedup": {
"branch": "master",
"git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
},
"untar": {
"branch": "master",
Expand All @@ -240,31 +240,31 @@
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"git_sha": "92793c143c93acd9129f15f35f25d3aab2b23c0e",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": [
"bam_sort_stats_samtools",
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
"bam_dedup_stats_samtools_umitools"
"bam_sort_stats_samtools"
]
},
"bedgraph_bedclip_bedgraphtobigwig": {
Expand All @@ -279,12 +279,12 @@
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "3e8b0c1144ccf60b7848efbdc2be285ff20b49ee",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
},
"fastq_subsample_fq_salmon": {
Expand Down
7 changes: 7 additions & 0 deletions modules/nf-core/fastp/environment.yml
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8 changes: 4 additions & 4 deletions modules/nf-core/fastp/main.nf
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4 changes: 3 additions & 1 deletion modules/nf-core/fastp/meta.yml
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