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Update all nf-core/modules in pipeline #1093

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merged 7 commits into from
Oct 13, 2023
Merged

Update all nf-core/modules in pipeline #1093

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a0f0602
Run nf-core modules update --all
drpatelh Oct 12, 2023
92eba51
Bump MultiQC version from 1.14 -> 1.15
drpatelh Oct 12, 2023
77145db
Fix channel issues after updating nf-core/modules
drpatelh Oct 12, 2023
e787b7a
[automated] Fix linting with Prettier
nf-core-bot Oct 12, 2023
12d8ac4
Update usage.md for igenomes warning
pinin4fjords Aug 30, 2023
22aab03
Fix merge conflicts
drpatelh Oct 13, 2023
ecefb97
Merge branch 'dev' into fixes
drpatelh Oct 13, 2023
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10 changes: 6 additions & 4 deletions CHANGELOG.md
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Expand Up @@ -23,17 +23,19 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
- [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
- [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage --genome
- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage use of `--genome`
- [PR #1078](https://github.com/nf-core/rnaseq/pull/1078) - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
- [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
- [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
- [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability

### Software dependencies

| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| `fastqc` | 0.11.9 | 0.12.1 |
| Dependency | Old version | New version |
| ----------------------- | ----------- | ----------- |
| `fastqc` | 0.11.9 | 0.12.1 |
| `multiqc` | 1.14 | 1.15 |
| `ucsc-bedgraphtobigwig` | 377 | 445 |

> **NB:** Dependency has been **updated** if both old and new version information is present.
>
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1 change: 1 addition & 0 deletions docs/usage.md
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Expand Up @@ -150,6 +150,7 @@ These files can then be specified to the workflow with the `--fasta` and `--gtf`
Notes:

- Compressed reference files are supported by the pipeline i.e. standard files with the `.gz` extension and indices folders with the `tar.gz` extension.

- If `--gff` is provided as input then this will be converted to a GTF file, or the latter will be used if both are provided.
- If `--gene_bed` is not provided then it will be generated from the GTF file.
- If `--additional_fasta` is provided then the features in this file (e.g. ERCC spike-ins) will be automatically concatenated onto both the reference FASTA file as well as the GTF annotation before building the appropriate indices.
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46 changes: 23 additions & 23 deletions modules.json
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Expand Up @@ -7,7 +7,7 @@
"nf-core": {
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
"git_sha": "de3e6fc949dcffb8d3508c015f435ace5773ff08",
"installed_by": ["modules"]
},
"cat/fastq": {
Expand All @@ -17,7 +17,7 @@
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
Expand Down Expand Up @@ -47,17 +47,17 @@
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"hisat2/align": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
"installed_by": ["fastq_align_hisat2"]
},
"hisat2/build": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
"installed_by": ["modules"]
},
"hisat2/extractsplicesites": {
Expand All @@ -67,7 +67,7 @@
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
"installed_by": ["bam_markduplicates_picard"]
},
"preseq/lcextrap": {
Expand All @@ -77,7 +77,7 @@
},
"qualimap/rnaseq": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
"installed_by": ["modules"]
},
"rsem/calculateexpression": {
Expand Down Expand Up @@ -137,17 +137,17 @@
},
"salmon/quant": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "c5b528d0a51c31621b485ab3bcc008f483619ea6",
"installed_by": ["modules", "fastq_subsample_fq_salmon"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
Expand Down Expand Up @@ -176,12 +176,12 @@
},
"star/align": {
"branch": "master",
"git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
"installed_by": ["modules"]
},
"stringtie/stringtie": {
Expand All @@ -201,17 +201,17 @@
},
"ucsc/bedclip": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "240937a2a9c30298110753292be041188891f2cb",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"umitools/extract": {
Expand All @@ -230,12 +230,12 @@
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
Expand All @@ -245,26 +245,26 @@
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": [
"bam_markduplicates_picard",
"bam_sort_stats_samtools",
"bam_markduplicates_picard",
"bam_dedup_stats_samtools_umitools"
]
},
"bedgraph_bedclip_bedgraphtobigwig": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"fastq_align_hisat2": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
Expand All @@ -279,7 +279,7 @@
},
"fastq_subsample_fq_salmon": {
"branch": "master",
"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
}
}
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6 changes: 3 additions & 3 deletions modules/local/multiqc/main.nf
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@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_medium'

conda "bioconda::multiqc=1.14"
conda "bioconda::multiqc=1.15"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
'biocontainers/multiqc:1.15--pyhdfd78af_0' }"

input:
path multiqc_config
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1 change: 1 addition & 0 deletions modules/nf-core/bbmap/bbsplit/main.nf
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6 changes: 3 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf
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37 changes: 37 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
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27 changes: 27 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
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10 changes: 7 additions & 3 deletions modules/nf-core/gunzip/main.nf
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5 changes: 3 additions & 2 deletions modules/nf-core/hisat2/align/main.nf
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6 changes: 3 additions & 3 deletions modules/nf-core/hisat2/build/main.nf
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4 changes: 4 additions & 0 deletions modules/nf-core/picard/markduplicates/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/qualimap/rnaseq/main.nf
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