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GET ALL THE THINGS WORKING WITH VERSIONS
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‎.github/workflows/ci.yml

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@@ -48,7 +48,6 @@ jobs:
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matrix:
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parameters:
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- "--skip_qc"
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- "--remove_ribo_rna --skip_qualimap"
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- "--skip_trimming"
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- "--gtf false"
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- "--star_index false"

‎.nf-core.yml

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@@ -10,11 +10,11 @@ lint:
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- modules/local/get_software_versions.nf
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update:
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nf-core/modules:
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rseqc/bamstat: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/inferexperiment: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/innerdistance: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/junctionannotation: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/junctionsaturation: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/readdistribution: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/readduplication: "906577873b66253b0d244871bfec2eeeaff73053"
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sortmerna: "906577873b66253b0d244871bfec2eeeaff73053"
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rseqc/bamstat: "7b3315591a149609e27914965f858c9a7e071564"
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rseqc/inferexperiment: "7b3315591a149609e27914965f858c9a7e071564"
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rseqc/innerdistance: "7b3315591a149609e27914965f858c9a7e071564"
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rseqc/junctionannotation: "7b3315591a149609e27914965f858c9a7e071564"
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rseqc/junctionsaturation: "7b3315591a149609e27914965f858c9a7e071564"
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rseqc/readdistribution: "7b3315591a149609e27914965f858c9a7e071564"
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rseqc/readduplication: "7b3315591a149609e27914965f858c9a7e071564"
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sortmerna: "7b3315591a149609e27914965f858c9a7e071564"

‎CHANGELOG.md

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@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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* [[#407](https://github.com/nf-core/rnaseq/issues/407)] - Filter mouse reads from PDX samples
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* [[#690](https://github.com/nf-core/rnaseq/issues/690)] - Error with post-trimmed read 2 sample names from FastQC in MultiQC
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* [[#693](https://github.com/nf-core/rnaseq/issues/693)] - Cutadapt version missing from MultiQC report
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* [[#697](https://github.com/nf-core/rnaseq/issues/697)] - pipeline_report.{txt,html} missing from pipeline_info directory
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* Added `python3` shebang to appropriate scripts in `bin/` directory
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@@ -25,6 +26,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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> **NB:** Parameter has been __added__ if just the new parameter information is present.
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> **NB:** Parameter has been __removed__ if parameter information isn't present.
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### Software dependencies
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Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
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| Dependency | Old version | New version |
34+
|---------------|-------------|-------------|
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| `hisat2` | 2.2.0 | 2.2.1 |
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| `picard` | 2.23.9 | 2.25.7 |
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| `salmon` | 1.4.0 | 1.5.2 |
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| `samtools` | 1.12 | 1.13 |
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| `trim-galore` | 0.6.6 | 0.6.7 |
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> **NB:** Dependency has been __updated__ if both old and new version information is present.
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> **NB:** Dependency has been __added__ if just the new version information is present.
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> **NB:** Dependency has been __removed__ if version information isn't present.
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## [[3.3](https://github.com/nf-core/rnaseq/releases/tag/3.3)] - 2021-07-29
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### Enhancements & fixes

‎CITATIONS.md

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## Pipeline tools
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* [BBMap](https://sourceforge.net/projects/bbmap/)
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* [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
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> Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
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‎README.md

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@@ -93,7 +93,7 @@ The nf-core/rnaseq pipeline comes with documentation about the pipeline [usage](
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These scripts were originally written for use at the [National Genomics Infrastructure](https://ngisweden.scilifelab.se), part of [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden, by Phil Ewels ([@ewels](https://github.com/ewels)) and Rickard Hammarén ([@Hammarn](https://github.com/Hammarn)).
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The pipeline was re-written in Nextflow DSL2 by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) at [The Francis Crick Institute](https://www.crick.ac.uk/), London.
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The pipeline was re-written in Nextflow DSL2 and is primarily maintained by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqeara Labs](https://seqera.io/), Spain.
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Many thanks to other who have helped out along the way too, including (but not limited to):
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[@Galithil](https://github.com/Galithil),

‎modules.json

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@@ -4,115 +4,115 @@
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"repos": {
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"nf-core/modules": {
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"bbmap/bbsplit": {
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"git_sha": "5b1cea7f7f38b78a8fd8e2b90b1b877bd117ed96"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"cat/fastq": {
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"git_sha": "b932210f270a1fea1f36c181abfb064448572846"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"custom/dumpsoftwareversions": {
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"git_sha": "22ec5c6007159d441585ef54bfa6272b6f93c78a"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"fastqc": {
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"git_sha": "ab67a1d41b63bf52fd7c147f7f8f6e8d167590b5"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"gffread": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"gunzip": {
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"git_sha": "3c5492b4a383ebd822422804d74cc9e15a747b0d"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"hisat2/align": {
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"git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"hisat2/build": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"hisat2/extractsplicesites": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"picard/markduplicates": {
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"git_sha": "e971f538a99bfa190f36f9303bede205e00b90a4"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"preseq/lcextrap": {
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"git_sha": "3c5492b4a383ebd822422804d74cc9e15a747b0d"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"qualimap/rnaseq": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rsem/calculateexpression": {
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"git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rsem/preparereference": {
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"git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/bamstat": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/inferexperiment": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/innerdistance": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/junctionannotation": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/junctionsaturation": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/readdistribution": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"rseqc/readduplication": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"salmon/index": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"salmon/quant": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"samtools/flagstat": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"samtools/idxstats": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"samtools/index": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"samtools/sort": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"samtools/stats": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"sortmerna": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"stringtie/stringtie": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"subread/featurecounts": {
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"git_sha": "c3687ef54bc0f651ea332c228317baf34c643c18"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"trimgalore": {
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"git_sha": "43c27792583b3db3faedf189adea48939e300cf2"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"ucsc/bedclip": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"ucsc/bedgraphtobigwig": {
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"git_sha": "9c31cf1566fa4f8660ac3973e02fe0caebe86235"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"umitools/dedup": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"umitools/extract": {
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"git_sha": "906577873b66253b0d244871bfec2eeeaff73053"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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},
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"untar": {
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"git_sha": "3c5492b4a383ebd822422804d74cc9e15a747b0d"
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"git_sha": "7b3315591a149609e27914965f858c9a7e071564"
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}
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}
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}

‎modules/local/bedtools_genomecov.nf

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output:
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tuple val(meta), path("*.forward.bedGraph"), emit: bedgraph_forward
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tuple val(meta), path("*.reverse.bedGraph"), emit: bedgraph_reverse
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

‎modules/local/cat_additional_fasta.nf

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output:
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path "${name}.fasta", emit: fasta
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path "${name}.gtf" , emit: gtf
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def genome_name = params.genome ? params.genome : fasta.getBaseName()

‎modules/local/deseq2_qc.nf

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path "*sample.dists_mqc.tsv", optional:true, emit: dists_multiqc
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path "*.log" , optional:true, emit: log
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path "size_factors" , optional:true, emit: size_factors
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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def label_lower = params.multiqc_label.toLowerCase()

‎modules/local/dupradar.nf

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tuple val(meta), path("*.pdf") , emit: pdf
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tuple val(meta), path("*.txt") , emit: txt
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tuple val(meta), path("*_mqc.txt"), emit: multiqc
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

‎modules/local/get_chrom_sizes.nf

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output:
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path '*.sizes' , emit: sizes
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path '*.fai' , emit: fai
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script:
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"""

‎modules/local/gtf2bed.nf

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output:
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path '*.bed' , emit: bed
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
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"""

‎modules/local/gtf_gene_filter.nf

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output:
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path "*.gtf" , emit: gtf
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script: // filter_gtf_for_genes_in_genome.py is bundled with the pipeline, in nf-core/rnaseq/bin/
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"""

‎modules/local/multiqc.nf

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path "*multiqc_report.html", emit: report
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path "*_data" , emit: data
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path "*_plots" , optional:true, emit: plots
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''

‎modules/local/multiqc_custom_biotype.nf

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@@ -23,7 +23,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
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output:
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tuple val(meta), path("*.tsv"), emit: tsv
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

‎modules/local/multiqc_custom_fail_mapped.nf

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output:
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path "*.tsv" , emit: tsv
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script:
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if (fail_mapped.size() > 0) {

‎modules/local/multiqc_custom_strand_check.nf

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output:
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path "*.tsv" , emit: tsv
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script:
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if (fail_strand.size() > 0) {

‎modules/local/rsem_merge_counts.nf

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path "rsem.merged.gene_tpm.tsv" , emit: tpm_gene
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path "rsem.merged.transcript_counts.tsv", emit: counts_transcript
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path "rsem.merged.transcript_tpm.tsv" , emit: tpm_transcript
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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"""

‎modules/local/salmon_merge_counts.nf

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path "salmon.merged.gene_counts_scaled.tsv" , emit: counts_gene_scaled
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path "salmon.merged.transcript_counts.tsv" , emit: counts_transcript
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path "salmon.merged.transcript_tpm.tsv" , emit: tpm_transcript
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script:
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"""

‎modules/local/salmon_summarizedexperiment.nf

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@@ -24,7 +24,7 @@ process SALMON_SUMMARIZEDEXPERIMENT {
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output:
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path "*.rds" , emit: rds
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
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"""

‎modules/local/salmon_tx2gene.nf

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@@ -23,7 +23,7 @@ process SALMON_TX2GENE {
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output:
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path "*.tsv" , emit: tsv
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
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"""

‎modules/local/salmon_tximport.nf

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Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ process SALMON_TXIMPORT {
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path "*gene_counts_scaled.tsv" , emit: counts_gene_scaled
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path "*transcript_tpm.tsv" , emit: tpm_transcript
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path "*transcript_counts.tsv" , emit: counts_transcript
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
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"""

‎modules/local/samplesheet_check.nf

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Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ process SAMPLESHEET_CHECK {
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output:
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path '*.csv' , emit: csv
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path "versions.yml", emit: version
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path "versions.yml", emit: versions
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script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
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"""

‎modules/local/star_align.nf

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Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ process STAR_ALIGN {
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tuple val(meta), path('*Log.final.out') , emit: log_final
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tuple val(meta), path('*Log.out') , emit: log_out
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tuple val(meta), path('*Log.progress.out'), emit: log_progress
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path "versions.yml" , emit: version
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path "versions.yml" , emit: versions
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tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted
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tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript

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