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Merge pull request #1093 from drpatelh/fixes
Update all nf-core/modules in pipeline
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‎CHANGELOG.md‎

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@@ -23,17 +23,19 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
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- [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
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- [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
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- [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
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- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage --genome
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- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage use of `--genome`
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- [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)
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- [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
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- [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
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- [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability
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### Software dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `fastqc` | 0.11.9 | 0.12.1 |
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| Dependency | Old version | New version |
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| ----------------------- | ----------- | ----------- |
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| `fastqc` | 0.11.9 | 0.12.1 |
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| `multiqc` | 1.14 | 1.15 |
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| `ucsc-bedgraphtobigwig` | 377 | 445 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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>

‎docs/usage.md‎

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@@ -150,6 +150,7 @@ These files can then be specified to the workflow with the `--fasta` and `--gtf`
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Notes:
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- Compressed reference files are supported by the pipeline i.e. standard files with the `.gz` extension and indices folders with the `tar.gz` extension.
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- 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.
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- If `--gene_bed` is not provided then it will be generated from the GTF file.
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- 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.

‎modules.json‎

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"nf-core": {
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"bbmap/bbsplit": {
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"branch": "master",
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"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
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"git_sha": "de3e6fc949dcffb8d3508c015f435ace5773ff08",
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"installed_by": ["modules"]
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},
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"cat/fastq": {
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
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"installed_by": ["modules"]
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},
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"custom/getchromsizes": {
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
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"installed_by": ["modules"]
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},
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"hisat2/align": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "a1881f6374506f9e031b7af814768cdb44a6a7d3",
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"installed_by": ["fastq_align_hisat2"]
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},
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"hisat2/build": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "f2f48836bf5c59434966a6c3b2211b29363f31ab",
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"installed_by": ["modules"]
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},
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"hisat2/extractsplicesites": {
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},
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"picard/markduplicates": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
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"installed_by": ["bam_markduplicates_picard"]
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},
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"preseq/lcextrap": {
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},
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"qualimap/rnaseq": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
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"installed_by": ["modules"]
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},
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"rsem/calculateexpression": {
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},
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"salmon/quant": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "c5b528d0a51c31621b485ab3bcc008f483619ea6",
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"installed_by": ["modules", "fastq_subsample_fq_salmon"]
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},
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"samtools/flagstat": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/idxstats": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
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"installed_by": ["bam_stats_samtools"]
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},
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"samtools/index": {
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},
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"star/align": {
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"branch": "master",
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"git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
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"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
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"installed_by": ["modules"]
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},
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"star/genomegenerate": {
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"branch": "master",
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"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
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"git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3",
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"installed_by": ["modules"]
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},
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"stringtie/stringtie": {
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},
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"ucsc/bedclip": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "240937a2a9c30298110753292be041188891f2cb",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"ucsc/bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
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"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
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},
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"umitools/dedup": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
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"installed_by": ["bam_dedup_stats_samtools_umitools"]
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},
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"umitools/extract": {
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"nf-core": {
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"bam_dedup_stats_samtools_umitools": {
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"branch": "master",
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"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"bam_markduplicates_picard": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"bam_rseqc": {
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},
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"bam_sort_stats_samtools": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["fastq_align_hisat2"]
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},
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"bam_stats_samtools": {
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"branch": "master",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": [
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools",
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"bam_markduplicates_picard",
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"bam_dedup_stats_samtools_umitools"
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]
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},
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"bedgraph_bedclip_bedgraphtobigwig": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"fastq_align_hisat2": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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},
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"fastq_fastqc_umitools_fastp": {
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},
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"fastq_subsample_fq_salmon": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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}
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}

‎modules/local/multiqc/main.nf‎

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

‎modules/nf-core/bbmap/bbsplit/main.nf‎

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‎modules/nf-core/custom/dumpsoftwareversions/main.nf‎

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‎modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test‎

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‎modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap‎

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‎modules/nf-core/gunzip/main.nf‎

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‎modules/nf-core/hisat2/align/main.nf‎

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