V1.0.0 release review fixes

.github/workflows/download_pipeline.yml

@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,7 +70,16 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true

CHANGELOG.md

@@ -36,6 +36,7 @@ Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/
 - [#45](https://github.com/nf-core/riboseq/pull/45) - Update CI from rnaseq, strip unused rnaseq components ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133))
 - [#48](https://github.com/nf-core/riboseq/pull/48) - Remove stub option from download in CI ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [#49](https://github.com/nf-core/riboseq/pull/49) - Fix CI ([@pinin4fjords](https://github.com/pinin4fjords), review by [@adamrtalbot](https://github.com/adamrtalbot))
+- [#50](https://github.com/nf-core/riboseq/pull/50) - V1.0.0 release review fixes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 
 ### `Dependencies`
 

CITATIONS.md

@@ -48,7 +48,7 @@
 
   > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
 
-- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
+- [Trim Galore!](https://github.com/FelixKrueger/TrimGalore)
 
 - [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Maxime U Garcia
+Copyright (c) Jonathan Manning
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -19,24 +19,24 @@
 
 ## Introduction
 
-**nf-core/riboseq** is a bioinformatics pipeline for analysis of ribo-seq data. It borrows heavily from nf-core/rnaseq in the preprocessing stages:
+**nf-core/riboseq** is a bioinformatics pipeline for analysis of Ribo-seq data. It borrows heavily from nf-core/rnaseq in the preprocessing stages:
 
 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
 2. Sub-sample FastQ files and auto-infer strandedness ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))
 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 4. UMI extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
-5. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
+5. Adapter and quality trimming ([`Trim Galore!`](https://github.com/FelixKrueger/TrimGalore))
 6. Removal of genome contaminants ([`BBSplit`](http://seqanswers.com/forums/showthread.php?t=41288))
 7. Removal of ribosomal RNA ([`SortMeRNA`](https://github.com/biocore/sortmerna))
-8. Multiple alignment to both genome and transcriptome using [`STAR`](https://github.com/alexdobin/STAR)
+8. Genome alignment of reads, outputting both genome and transcriptome alignments with [`STAR`](https://github.com/alexdobin/STAR)
 9. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
 10. UMI-based deduplication ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
 
 Differences occur in the downstream analysis steps. Currently these specialist steps are:
 
 1. Check reads distribution around annotated protein coding regions on user provided transcripts, show frame bias and estimate P-site offset for different group of reads ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
-2. Predict translating open reading frames and/ or translation initiation sites _de novo_ from alignment data ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
-3. Derive candidate ORFs from reference data and detect translating ORFs from that list ([`Ribotricer`](https://github.com/smithlabcode/ribotricer))
+2. (default, optional) Predict translated open reading frames and/ or translation initiation sites _de novo_ from alignment data ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
+3. (default, optional) Derive candidate ORFs from reference data and detect translated ORFs from that list ([`Ribotricer`](https://github.com/smithlabcode/ribotricer))
 4. (optional) Use a translational efficiency approach to study the dynamics of transcription and translation, with [anota2seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html). **requires matched RNA-seq and Ribo-seq data**
 
 ## Usage
@@ -53,7 +53,7 @@ sample,fastq_1,fastq_2,strandedness,type
 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward,riboseq
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Each row should have a 'type' value of `riboseq`, `tiseq` or `rnaseq`. Future iterations of the workflow will conduct paired analysis of matched riboseq and rnaseq samples to accomplish analysis types such as 'translational efficiency, but in the current version you should set this to `riboseq` or `tiseq` for reglar ribo-seq or TI-seq data respectively.
+Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Each row should have a 'type' value of `riboseq`, `tiseq` or `rnaseq`. Future iterations of the workflow will conduct paired analysis of matched riboseq and rnaseq samples to accomplish analysis types such as 'translational efficiency, but in the current version you should set this to `riboseq` or `tiseq` for reglar Ribo-seq or TI-seq data respectively.
 
 Now, you can run the pipeline using:
 
@@ -98,10 +98,10 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/riboseq was originally written by [Jonathan Manning](https://github.com/pinin4fjords) (Bioinformatics Engineer as Seqera) with support from [Altos labs](https://www.altoslabs.com/) and in discussion with [Felix Krueger](https://github.com/FelixKrueger) and [Christel Krueger](https://github.com/ChristelKrueger). We thank the following people for their input:
+nf-core/riboseq was originally written by [Jonathan Manning](https://github.com/pinin4fjords) (Bioinformatics Engineer at Seqera) with support from [Altos Labs](https://www.altoslabs.com/) and in discussion with [Felix Krueger](https://github.com/FelixKrueger) and [Christel Krueger](https://github.com/ChristelKrueger). We thank the following people for their input:
 
 - Anne Bresciani (ZS)
-- [Felibe Almeida](https://github.com/fmalmeida) (ZS)
+- [Felipe Almeida](https://github.com/fmalmeida) (ZS)
 - [Mikhail Osipovitch](https://github.com/mosi223) (ZS)
 - [Edward Wallace](https://github.com/ewallace) (University of Edinburgh)
 - [Jack Tierney](https://github.com/JackCurragh) (University College Cork)

assets/email_template.html

@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/riboseq: Analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting)">
+  <meta name="description" content="nf-core/riboseq: Analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting)">
   <title>nf-core/riboseq Pipeline Report</title>
 </head>
 <body>

conf/base.config

@@ -15,7 +15,7 @@ process {
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 1
+    maxRetries    = 2
     maxErrors     = '-1'
 
     // Process-specific resource requirements

docs/output.md

@@ -356,7 +356,7 @@ By plotting fold changes for RNA-seq and Ribo-seq data against one another this
 <details markdown="1">
 <summary>Output files</summary>
 
-- `multiqc/<ALIGNER>/`
+- `multiqc/`
   - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
   - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
 

docs/usage.md

@@ -71,9 +71,9 @@ When specifying `contrasts` to perform a translational efficiency analysis (see
 
 The pipeline currently uses [STAR](https://github.com/alexdobin/STAR) to map the raw FastQ reads to the reference genome and project the alignments onto the transcriptome. STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome.
 
-### Unique Molecular Identifiers (UMI)
+### Unique Molecular Identifiers (UMIs)
 
-The pipeline supports Unique Molecular Identifiers to increase the accuracy of the quantification. UMIs are short sequences used to uniquely tag each molecule in a sample library and facilitate the accurate identification of read duplicates. They must be added during library preparation and prior to sequencing, therefore require appropriate arrangements with your sequencing provider.
+The pipeline supports UMIs to increase the accuracy of the quantification. UMIs are short sequences used to uniquely tag each molecule in a sample library and facilitate the accurate identification of read duplicates. They must be added during library preparation and prior to sequencing, therefore require appropriate arrangements with your sequencing provider.
 
 To take UMIs into consideration during a workflow run, specify the `--with_umi` parameter. The pipeline currently supports UMIs, which are embedded within a read's sequence and UMIs, whose sequence is given inside the read's name. Please consult your kit's manual and/or contact your sequencing provider regarding the exact specification.
 

nextflow.config

@@ -50,7 +50,6 @@ params {
     skip_bbsplit               = true
 
     // Ribosomal RNA removal
-    sortmerna_index            = false
     remove_ribo_rna            = true
     save_non_ribo_reads        = false
     ribo_database_manifest     = "${projectDir}/assets/rrna-db-defaults.txt"
@@ -61,7 +60,6 @@ params {
     seq_center                 = null
     bam_csi_index              = false
     star_ignore_sjdbgtf        = false
-    salmon_index               = null
     salmon_quant_libtype       = null
     min_mapped_reads           = 5
     extra_star_align_args      = null
@@ -297,9 +295,9 @@ dag {
 
 manifest {
     name            = 'nf-core/riboseq'
-    author          = """Maxime U Garcia"""
+    author          = """Jonathan Manning"""
     homePage        = 'https://github.com/nf-core/riboseq'
-    description     = """Analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting)"""
+    description     = """Analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting)"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
     version         = '1.0.0'

nextflow_schema.json

@@ -2,7 +2,7 @@
     "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/riboseq/master/nextflow_schema.json",
     "title": "nf-core/riboseq pipeline parameters",
-    "description": "Analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting)",
+    "description": "Analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting)",
     "type": "object",
     "definitions": {
         "input_output_options": {