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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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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [PR #1103](https://github.com/nf-core/rnaseq/issues/1103) - Updates FASTQC and UMITOOLS modules and their dependencies which have had their version string extraction commands updated.

### Software dependencies

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### Modules / Subworkflows
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44 changes: 22 additions & 22 deletions modules.json
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Expand Up @@ -27,12 +27,12 @@
},
"fastp": {
"branch": "master",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"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 Down Expand Up @@ -152,31 +152,31 @@
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"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": {
"branch": "master",
"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"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"]
},
"umitools/extract": {
"branch": "master",
"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 @@ -240,12 +240,12 @@
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
Expand All @@ -255,16 +255,16 @@
},
"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": {
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7 changes: 7 additions & 0 deletions modules/nf-core/fastp/environment.yml
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2 changes: 1 addition & 1 deletion 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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