Merge branch 'kallisto_quant' of github.com:nf-core/rnaseq into kallisto_quant

Author: pinin4fjords

CHANGELOG.md

@@ -10,10 +10,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Special thanks to the following for their contributions to the release:
 
 - [Adam Talbot](https://github.com/adamrtalbot)
+- [Jonathan Manning](https://github.com/pinin4fjords)
 - [Júlia Mir Pedrol](https://github.com/mirpedrol)
 - [Matthias Zepper](https://github.com/MatthiasZepper)
 - [Maxime Garcia](https://github.com/maxulysse)
-- [Jonathan Manning](https://github.com/pinin4fjords)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
@@ -38,7 +38,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 | Dependency              | Old version | New version |
 | ----------------------- | ----------- | ----------- |
 | `fastqc`                | 0.11.9      | 0.12.1      |
-| `multiqc`               | 1.14        | 1.15        |
+| `multiqc`               | 1.14        | 1.17        |
 | `ucsc-bedgraphtobigwig` | 377         | 445         |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
@@ -65,7 +65,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 ### Enhancements & fixes
 
 - [[#1011](https://github.com/nf-core/rnaseq/issues/1011)] - FastQ files from UMI-tools not being passed to fastp
-- [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudo-alignment to only run pre-processing QC steps.
+- [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudoalignment to only run pre-processing QC steps.
 - [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)
 - [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
 - [PR #1038](https://github.com/nf-core/rnaseq/pull/1038) - Updated error log for count values when supplying `--additional_fasta`
@@ -813,7 +813,7 @@ Major novel changes include:
 - Added options to skip several steps
   - Skip trimming using `--skipTrimming`
   - Skip BiotypeQC using `--skipBiotypeQC`
-  - Skip Alignment using `--skipAlignment` to only use pseudo-alignment using Salmon
+  - Skip Alignment using `--skipAlignment` to only use pseudoalignment using Salmon
 
 ### Documentation updates
 

README.md

@@ -39,7 +39,7 @@
     3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html)
     4. [`Preseq`](http://smithlabresearch.org/software/preseq/)
     5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
-15. Pseudo-alignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_)
+15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_)
 16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))
 
 > **Note**

assets/multiqc_config.yml

@@ -67,6 +67,7 @@ extra_fn_clean_exts:
   - ".umi_dedup"
   - "_val"
   - ".markdup"
+  - "_primary"
 
 # Customise the module search patterns to speed up execution time
 #  - Skip module sub-tools that we are not interested in

bin/summarizedexperiment.r

@@ -2,7 +2,7 @@
 
 library(SummarizedExperiment)
 
-## Create SummarizedExperiment (se) object from Salmon counts
+## Create SummarizedExperiment (se) object from counts
 
 args <- commandArgs(trailingOnly = TRUE)
 if (length(args) < 3) {

conf/modules.config

@@ -705,11 +705,9 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
     if (!params.skip_qc & !params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC_STAR_SALMON' {
-                ext.prefix = "deseq2"
                 ext.args   = { [
                     "--id_col 1",
                     "--sample_suffix ''",
-                    "--outprefix deseq2",
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }
@@ -770,11 +768,9 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
     if (!params.skip_qc & !params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC_RSEM' {
-                ext.prefix = "deseq2"
                 ext.args   = { [
                     "--id_col 1",
                     "--sample_suffix ''",
-                    "--outprefix deseq2",
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }
@@ -1085,10 +1081,10 @@ if (!params.skip_multiqc) {
 }
 
 //
-// Salmon/ Kallisto pseudo-alignment options
+// Salmon/ Kallisto pseudoalignment options
 //
 
-if (params.pseudo_aligner == 'salmon') {
+if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
     process {
 
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' {
@@ -1102,15 +1098,14 @@ if (params.pseudo_aligner == 'salmon') {
     }
 }
 
-if (params.pseudo_aligner == 'kallisto') {
+if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
     process {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT' {
             ext.args = params.extra_kallisto_quant_args ?: ''
-
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_run_info.json') ? null : filename }
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.run_info.json') || filename.endsWith('.log.txt') ? null : filename }
             ]
         }
     }
@@ -1150,7 +1145,6 @@ if (!params.skip_pseudo_alignment) {
                 ext.args   = { [
                     "--id_col 1",
                     "--sample_suffix ''",
-                    "--outprefix deseq2",
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }

docs/output.md

@@ -41,9 +41,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [featureCounts](#featurecounts) - Read counting relative to gene biotype
   - [DESeq2](#deseq2) - PCA plot and sample pairwise distance heatmap and dendrogram
   - [MultiQC](#multiqc) - Present QC for raw reads, alignment, read counting and sample similiarity
-- [Pseudo-alignment and quantification](#pseudo-alignment-and-quantification)
-  - [Salmon](#salmon) - Wicked fast gene and isoform quantification relative to the transcriptome
-  - [Kallisto](#kallisto) - Near-optimal probabilistic RNA-seq quantification
+- [Pseudoalignment and quantification](#pseudoalignment-and-quantification)
+  - [Salmon](#pseudoalignment) - Wicked fast gene and isoform quantification relative to the transcriptome
+  - [Kallisto](#pseudoalignment) - Near-optimal probabilistic RNA-seq quantification
     Wicked fast gene and isoform quantification relative to the transcriptome
 - [Workflow reporting and genomes](#workflow-reporting-and-genomes)
   - [Reference genome files](#reference-genome-files) - Saving reference genome indices/files
@@ -205,7 +205,7 @@ The STAR section of the MultiQC report shows a bar plot with alignment rates: go
 
 ![MultiQC - STAR alignment scores plot](images/mqc_star.png)
 
-[Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) from [Ocean Genomics](https://oceangenomics.com/) and [Kallisto](https://pachterlab.github.io/kallisto/), from the Pachter Lab, are provided as options for pseudo-alignment. Both allow quantification of reads against an index generated from a reference set of target transcripts. By default, the transcriptome-level BAM files generated by STAR are provided to Salmon for downstream quantification, and Kallisto is not an option here (it does not allow BAM file input). But you can provide FASTQ files directly as input to either Salmon or Kallisto in order to pseudo-align and quantify your data by providing the `--pseudo_aligner (salmon or kallisto)` parameter. See the [Salmon](#salmon) and (Kallisto)[#kallisto] results sections for more details.
+[Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) from [Ocean Genomics](https://oceangenomics.com/) and [Kallisto](https://pachterlab.github.io/kallisto/), from the Pachter Lab, are provided as options for pseudoalignment. Both allow quantification of reads against an index generated from a reference set of target transcripts. By default, the transcriptome-level BAM files generated by STAR are provided to Salmon for downstream quantification, and Kallisto is not an option here (it does not allow BAM file input). But you can provide FASTQ files directly as input to either Salmon or Kallisto in order to pseudoalign and quantify your data by providing the `--pseudo_aligner salmon` or `--pseudo_aligner kallisto` parameter. See the [Salmon](#pseudoalignment) and [Kallisto](#pseudoalignment) results sections for more details.
 
 ### STAR via RSEM
 
@@ -670,9 +670,9 @@ The plot on the left hand side shows the standard PC plot - notice the variable
 
 Results generated by MultiQC collate pipeline QC from supported tools i.e. FastQC, Cutadapt, SortMeRNA, STAR, RSEM, HISAT2, Salmon, SAMtools, Picard, RSeQC, Qualimap, Preseq and featureCounts. Additionally, various custom content has been added to the report to assess the output of dupRadar, DESeq2 and featureCounts biotypes, and to highlight samples failing a mimimum mapping threshold or those that failed to match the strand-specificity provided in the input samplesheet. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
-## Pseudo-alignment and quantification
+## Pseudoalignment and quantification
 
-### Pseudo-alignment
+### Pseudoalignment
 
 The principal output files are the same between Salmon and Kallsto:
 
@@ -717,10 +717,10 @@ An additional subset of files are distinct to each tool, for Salmon:
   - `abundance.h5`: a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length. This file can be read in by [sleuth](https://pachterlab.github.io/sleuth/about).
   - `abundance.tsv`: a plaintext file of the abundance estimates. It does not contains bootstrap estimates.
   - `run_info.json`: a json file containing information about the run.
-- `<SAMPLE>.log.txt`: standard output from the Kallisto process per sample.
-</details>
+  - `kallisto_quant.log`: standard output from the Kallisto process per sample.
+  </details>
 
-As described in the [STAR and Salmon](#star-and-salmon) section, you can choose to pseudo-align and quantify your data with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by providing the `--pseudo_aligner` parameter. By default, Salmon is run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon or Kallisto in isolation. If Salmon or Kallisto are run in isolation, the outputs mentioned above will be found in a folder named `salmon` or `kallisto`. If Salmon is run alongside STAR, the folder will be named `star_salmon`.
+As described in the [STAR and Salmon](#star-and-salmon) section, you can choose to pseudoalign and quantify your data with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by providing the `--pseudo_aligner` parameter. By default, Salmon is run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon or Kallisto in isolation. If Salmon or Kallisto are run in isolation, the outputs mentioned above will be found in a folder named `salmon` or `kallisto`. If Salmon is run alongside STAR, the folder will be named `star_salmon`.
 
 Transcripts with large inferential uncertainty won't be assigned the exact number of reads reproducibly, every time Salmon is run. Read more about this on the [nf-core/rnaseq](https://github.com/nf-core/rnaseq/issues/585) and [salmon](https://github.com/COMBINE-lab/salmon/issues/613) Github repos.