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Update all nf-core/modules and subworkflows #1330

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merged 15 commits into from
Jun 28, 2024
Merged

Update all nf-core/modules and subworkflows #1330

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b89fac3
Merge pull request #1156 from nf-core/dev
drpatelh Jan 8, 2024
8acf634
Update all nf-core modules and subworkflows
drpatelh Jun 20, 2024
961c9b6
Fix pipeline after updates to GFFREAD module
drpatelh Jun 20, 2024
51939f2
Update CHANGELOG
drpatelh Jun 20, 2024
1333342
Update snapshots for prepare_genome subworkflow
drpatelh Jun 20, 2024
b8cf404
Remove problem multiqc setting
pinin4fjords Jun 20, 2024
d338f00
Revert "Remove problem multiqc setting"
pinin4fjords Jun 21, 2024
5bb52da
Merge branch 'updates' of github.com:drpatelh/nf-core-rnaseq into upd…
pinin4fjords Jun 25, 2024
e640eea
Update all nf-core/modules again
drpatelh Jun 27, 2024
6035f5b
Rename custom content keys as required in MultiQC v1.22.3
drpatelh Jun 27, 2024
0aaf228
Update snapshots for default pipeline test
drpatelh Jun 27, 2024
5818d6c
Merge branch 'updates' of github.com:drpatelh/nf-core-rnaseq into upd…
pinin4fjords Jun 27, 2024
489e7fd
patch dupradar
pinin4fjords Jun 27, 2024
2d314bf
Fix syntax
pinin4fjords Jun 27, 2024
e7ba0cf
update snapshot
pinin4fjords Jun 28, 2024
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6 changes: 4 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -95,6 +95,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file
- [PR #1328](https://github.com/nf-core/rnaseq/pull/1328) - Add pipeline level test for STAR-RSEM and HISAT2
- [PR #1329](https://github.com/nf-core/rnaseq/pull/1329) - Remove tags from all nf-test files
- [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows

### Parameters

Expand All @@ -114,9 +115,10 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
| `bioconductor-dupradar` | 1.28.0 | 1.32.0 |
| `bioconductor-summarizedexperiment` | 1.24.0 | 1.32.0 |
| `bioconductor-tximeta` | 1.12.0 | 1.20.1 |
| `multiqc` | 1.20 | 1.21 |
| `gffread` | 0.12.1 | 0.12.7 |
| `multiqc` | 1.20 | 1.22.3 |
| `picard` | 3.0.0 | 3.1.1 |
| `samtools` | 1.17 | 1.19.2 |
| `samtools` | 1.17 | 1.20 |
| `sortmerna` | 4.3.4 | 4.3.6 |
| `umi_tools` | 1.14 | 1.15 |

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3 changes: 1 addition & 2 deletions bin/mqc_features_stat.py
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Expand Up @@ -21,8 +21,7 @@
# description: '% reads overlapping {ft} features'
# max: 100
# min: 0
# scale: 'RdYlGn-rev'
# format: '{{:.2f}}%'"""
# scale: 'RdYlGn-rev'"""


def mqc_feature_stat(bfile, features, outfile, sname=None):
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53 changes: 27 additions & 26 deletions modules.json
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Expand Up @@ -7,7 +7,7 @@
"nf-core": {
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "ecc2139bc014be1d0117d6c69458d82fbfa3328f",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"bedtools/genomecov": {
Expand All @@ -17,32 +17,33 @@
},
"cat/fastq": {
"branch": "master",
"git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca",
"git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
"installed_by": ["modules"]
},
"custom/catadditionalfasta": {
"branch": "master",
"git_sha": "ba6ec49354837595649acd84e7a867d59bf11ad0",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "1b0ffa4e5aed5b7e3cd4311af31bd3b2c8345051",
"git_sha": "41a4135c502b42ede663af87efa70a96ecbd7cb9",
"installed_by": ["modules"]
},
"custom/tx2gene": {
"branch": "master",
"git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a",
"git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
"installed_by": ["modules", "quantify_pseudo_alignment"]
},
"dupradar": {
"branch": "master",
"git_sha": "f632a6e25b05497477920183cff33ba72ab7b6fc",
"installed_by": ["modules"]
"patch": "modules/nf-core/dupradar/dupradar.diff"
},
"fastp": {
"branch": "master",
"git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
"git_sha": "b90b5cd93149a1b3be263d916c7234fe0708a71c",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
Expand All @@ -52,32 +53,32 @@
},
"fq/subsample": {
"branch": "master",
"git_sha": "59d1faf07ace4f7a00f7fa7778bce4e1f1dcdd63",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["fastq_subsample_fq_salmon", "modules"]
},
"gffread": {
"branch": "master",
"git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
"git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
"git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
"installed_by": ["modules"]
},
"hisat2/align": {
"branch": "master",
"git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["fastq_align_hisat2"]
},
"hisat2/build": {
"branch": "master",
"git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"hisat2/extractsplicesites": {
"branch": "master",
"git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"kallisto/index": {
Expand All @@ -92,7 +93,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"git_sha": "314d742bdb357a1df5f9b88427b3b6ac78aa33f7",
"installed_by": ["modules"]
},
"picard/markduplicates": {
Expand All @@ -102,7 +103,7 @@
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "9a88058962c0ee1715f2ad0e017c37e0cd75e532",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"qualimap/rnaseq": {
Expand Down Expand Up @@ -172,17 +173,17 @@
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": [
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
Expand All @@ -191,12 +192,12 @@
},
"samtools/sort": {
"branch": "master",
"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": ["bam_stats_samtools"]
},
"sortmerna": {
Expand Down Expand Up @@ -231,7 +232,7 @@
},
"trimgalore": {
"branch": "master",
"git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744",
"git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"tximeta/tximport": {
Expand Down Expand Up @@ -275,12 +276,12 @@
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
Expand All @@ -290,12 +291,12 @@
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": ["fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"installed_by": [
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
Expand All @@ -309,12 +310,12 @@
},
"fastq_align_hisat2": {
"branch": "master",
"git_sha": "701ae347c4508fba1b7d65262596f278b6a11cb6",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "e98edb838fb0072c0783139ed16723bbc5d48d23",
"git_sha": "b90b5cd93149a1b3be263d916c7234fe0708a71c",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
Expand Down
19 changes: 19 additions & 0 deletions modules/nf-core/bbmap/bbsplit/main.nf
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97 changes: 97 additions & 0 deletions modules/nf-core/bbmap/bbsplit/tests/main.nf.test
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