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Merge pull request #1036 from drpatelh/updates
Fix #1011
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‎CHANGELOG.md‎

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### Enhancements & fixes
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- [[#1011](https://github.com/nf-core/rnaseq/issues/1011)] - FastQ files from UMI-tools not being passed to fastp
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- [PR #1016](https://github.com/nf-core/rnaseq/pull/1016) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
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- [PR #1025](https://github.com/nf-core/fetchngs/pull/1025) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
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### Software dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `fastp` | 0.23.2 | 0.23.4 |
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| `samtools` | 1.16.1 | 1.17 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.

‎conf/test.config‎

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input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv"
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// Genome references
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta"
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gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz"
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transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta"
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additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz"
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bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt"
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hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz"
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salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz"
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rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz"
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta"
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gtf = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gff.gz"
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transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/transcriptome.fasta"
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additional_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/gfp.fa.gz"
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bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/bbsplit_fasta_list.txt"
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hisat2_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/hisat2.tar.gz"
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salmon_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/salmon.tar.gz"
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rsem_index = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz"
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// Other parameters
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skip_bbsplit = false

‎conf/test_cache.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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Nextflow config file for running minimal tests using cached / offline test data
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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‎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": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
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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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"fastp": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["modules", "fastq_fastqc_umitools_fastp"]
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"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
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"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
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},
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"fastqc": {
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"branch": "master",
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},
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"hisat2/align": {
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"branch": "master",
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"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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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": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"installed_by": ["modules"]
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},
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"hisat2/extractsplicesites": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"installed_by": ["modules"]
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},
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"picard/markduplicates": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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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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"samtools/stats": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"installed_by": ["bam_stats_samtools"]
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},
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"sortmerna": {
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},
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"star/align": {
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"branch": "master",
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"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
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"git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
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"installed_by": ["modules"]
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},
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"star/genomegenerate": {
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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": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
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"installed_by": ["subworkflows"]
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},
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"bam_markduplicates_picard": {
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},
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"bam_sort_stats_samtools": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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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": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
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"installed_by": [
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"bam_dedup_stats_samtools_umitools",
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"bam_markduplicates_picard",
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"bam_sort_stats_samtools",
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"bam_dedup_stats_samtools_umitools"
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"bam_sort_stats_samtools"
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]
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},
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"bedgraph_bedclip_bedgraphtobigwig": {
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},
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"fastq_fastqc_umitools_fastp": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "48dbb403fb2849b3d2c6c2e3eaaedbcca799428d",
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"installed_by": ["subworkflows"]
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},
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"fastq_fastqc_umitools_trimgalore": {

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

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‎modules/nf-core/bbmap/bbsplit/meta.yml‎

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‎modules/nf-core/fastp/main.nf‎

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

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‎modules/nf-core/hisat2/align/meta.yml‎

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

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