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Merge pull request #1093 from drpatelh/fixes
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Update all nf-core/modules in pipeline
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drpatelh authored Oct 13, 2023
2 parents c742192 + ecefb97 commit 4f212b3
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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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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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