diff --git a/CHANGELOG.md b/CHANGELOG.md index ce1ec2e55..1086131ef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ Special thanks to the following for their contributions to the release: - [PR #1597](https://github.com/nf-core/rnaseq/pull/1597) - Bump version after release 3.20.0 - [PR #1603](https://github.com/nf-core/rnaseq/pull/1603) - Add bam input pathway +- [PR #1604](https://github.com/nf-core/rnaseq/pull/1604) - Enable BAM input for RSEM ## [[3.20.0](https://github.com/nf-core/rnaseq/releases/tag/3.20.0)] - 2025-08-18 diff --git a/conf/test.config b/conf/test.config index 06f9856a5..1b3bd5db8 100644 --- a/conf/test.config +++ b/conf/test.config @@ -35,7 +35,6 @@ params { bbsplit_fasta_list = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt' hisat2_index = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz' salmon_index = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz' - rsem_index = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz' // Other parameters skip_bbsplit = false diff --git a/docs/output.md b/docs/output.md index c29def655..b47593a05 100644 --- a/docs/output.md +++ b/docs/output.md @@ -11,7 +11,7 @@ nextflow run nf-core/rnaseq -profile test_full, The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. :::tip -Many of the BAM files produced by this pipeline can be reused as input for future runs. This is particularly useful for reprocessing data or running downstream analysis steps without repeating computationally expensive alignment. See the [usage documentation](https://nf-co.re/rnaseq/usage#using-bam-files-as-input) for details on using BAM files as input. +Many of the BAM files produced by this pipeline can be reused as input for future runs with `--skip_alignment`. This is particularly useful for reprocessing data or running downstream analysis steps without repeating computationally expensive alignment. See the [usage documentation](https://nf-co.re/rnaseq/usage#bam-input-for-reprocessing-workflow) for details on using BAM files as input. ::: ## Pipeline overview @@ -280,8 +280,8 @@ The STAR section of the MultiQC report shows a bar plot with alignment rates: go - `rsem.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples. - `*.genes.results`: RSEM gene-level quantification results for each sample. - `*.isoforms.results`: RSEM isoform-level quantification results for each sample. - - `*.STAR.genome.bam`: If `--save_align_intermeds` is specified the original BAM file containing read alignments to the reference genome will be placed in this directory. These files can be reused as `genome_bam` input in future pipeline runs. - - `*.transcript.bam`: If `--save_align_intermeds` is specified the original BAM file containing read alignments to the transcriptome will be placed in this directory. These files can be reused as `transcriptome_bam` input in future pipeline runs. + - `*.STAR.genome.bam`: If `--save_align_intermeds` is specified the BAM file from STAR alignment containing read alignments to the reference genome will be placed in this directory. These files can be reused as `genome_bam` input in future pipeline runs. + - `*.transcript.bam`: If `--save_align_intermeds` is specified the BAM file from STAR alignment containing read alignments to the transcriptome will be placed in this directory. These files can be reused as `transcriptome_bam` input in future pipeline runs. - `star_rsem/.stat/` - `*.cnt`, `*.model`, `*.theta`: RSEM counts and statistics for each sample. - `star_rsem/log/` @@ -289,7 +289,7 @@ The STAR section of the MultiQC report shows a bar plot with alignment rates: go -[RSEM](https://github.com/deweylab/RSEM) is a software package for estimating gene and isoform expression levels from RNA-seq data. It has been widely touted as one of the most accurate quantification tools for RNA-seq analysis. RSEM wraps other popular tools to map the reads to the genome (i.e. STAR, Bowtie2, HISAT2; STAR is used in this pipeline) which are then subsequently filtered relative to a transcriptome before quantifying at the gene- and isoform-level. Other advantages of using RSEM are that it performs both the alignment and quantification in a single package and its ability to effectively use ambiguously-mapping reads. +[RSEM](https://github.com/deweylab/RSEM) is a software package for estimating gene and isoform expression levels from RNA-seq data. It has been widely touted as one of the most accurate quantification tools for RNA-seq analysis. When using `--aligner star_rsem`, the pipeline first runs STAR alignment with RSEM-compatible parameters to generate genome and transcriptome BAM files, then RSEM quantifies expression using these pre-aligned BAMs via the `--alignments` mode. This approach ensures optimal compatibility while maintaining RSEM's ability to effectively use ambiguously-mapping reads. You can choose to align and quantify your data with RSEM by providing the `--aligner star_rsem` parameter. @@ -869,7 +869,7 @@ A number of genome-specific files are generated by the pipeline because they are - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - Parameters used by the pipeline run: `params.json`. - `samplesheets/` - - `samplesheet_with_bams.csv`: **Auto-generated complete samplesheet** (only created when using `--save_align_intermeds`) containing all samples with BAM file paths. For samples processed from FASTQ, includes paths to newly generated BAMs; for samples that were BAM input, preserves the original input paths. This comprehensive samplesheet can be used directly for future pipeline runs, enabling efficient reprocessing without re-alignment. + - `samplesheet_with_bams.csv`: **Auto-generated samplesheet for BAM reprocessing** (only created when using `--save_align_intermeds`) containing all samples with BAM file paths. For samples processed from FASTQ, includes paths to newly generated BAMs; for samples that were BAM input, preserves the original input paths. This samplesheet can be used directly for future pipeline runs with `--skip_alignment`, enabling efficient reprocessing without re-alignment. diff --git a/docs/usage.md b/docs/usage.md index 294e891fe..00cac88b2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -136,7 +136,7 @@ nextflow run nf-core/rnaseq \ -profile docker ``` -The pipeline will skip alignment and indexing steps, putting the BAM files through post-processing and quantification only. +The `--skip_alignment` flag tells the pipeline to skip alignment, and in this situation it will use any provided BAM files instead of performing alignment, putting them through post-processing and quantification only. #### Example of generated samplesheet @@ -152,11 +152,15 @@ SAMPLE2,/path/sample2_R1.fastq.gz,,reverse,results/star_salmon/SAMPLE2.sorted.ba > **⚠️ Warning**: This feature is designed specifically for BAM files generated by this pipeline. Using arbitrary BAM files from other sources is **not officially supported** and will likely only work via the two-step workflow described above. Users attempting to use other BAMs do so at their own risk. +> **⚠️ Warning**: You cannot mix quantifier types between BAM generation and reprocessing runs. BAM files generated with `--aligner star_salmon` must be reprocessed with `--aligner star_salmon`. Similarly, BAM files from `--aligner star_rsem` must be reprocessed with `--aligner star_rsem`. Mixing quantifier types will likely produce incorrect results due to incompatible alignment parameters. + **Key technical details:** +- BAM files are only used when `--skip_alignment` is specified - The pipeline automatically indexes provided BAM files - You can provide just `genome_bam`, just `transcriptome_bam`, or both -- Mixed samplesheets (some samples with FASTQ, others with BAM) are supported +- Mixed samplesheets are supported, but samples with BAM files require `--skip_alignment` +- Without `--skip_alignment`, the pipeline will perform alignment even if BAM files are provided - For BAM file locations from pipeline outputs, see the [output documentation](https://nf-co.re/rnaseq/output) This workflow is ideal for tweaking downstream processing steps (quantification methods, QC parameters, differential expression analysis) without repeating time-consuming alignment. @@ -181,7 +185,7 @@ If you would like to reduce the number of reads used in the analysis, for exampl The `--aligner hisat2` option is not currently supported using ARM architecture ('-profile arm') ::: -By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. +By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Both `--aligner star_salmon` and `--aligner star_rsem` use STAR for alignment, so you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. You also have the option to pseudoalign and quantify your data directly with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by specifying `salmon` or `kallisto` to the `--pseudo_aligner` parameter. The selected pseudoaligner will then be 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. By default, the pipeline will use the genome fasta and gtf file to generate the transcripts fasta file, and then to build the Salmon index. You can override these parameters using the `--transcript_fasta` and `--salmon_index` parameters, respectively. @@ -313,7 +317,7 @@ Notes: - 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. - If `--gene_bed` is not provided then it will be generated from the GTF file. - 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. -- When using `--aligner star_rsem`, both the STAR and RSEM indices should be present in the path specified by `--rsem_index` (see [#568](https://github.com/nf-core/rnaseq/issues/568)). +- When using `--aligner star_rsem`, the pipeline will build separate STAR and RSEM indices. STAR performs alignment with RSEM-compatible parameters, then RSEM quantifies from the resulting BAM files using `--alignments` mode. - If the `--skip_alignment` option is used along with `--transcript_fasta`, the pipeline can technically run without providing the genomic FASTA (`--fasta`). However, this approach is **not recommended** with `--pseudo_aligner salmon`, as any dynamically generated Salmon index will lack decoys. To ensure optimal indexing with decoys, it is **highly recommended** to include the genomic FASTA (`--fasta`) with Salmon, unless a pre-existing decoy-aware Salmon index is supplied. For more details on the benefits of decoy-aware indexing, refer to the [Salmon documentation](https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode). #### Reference genome diff --git a/modules.json b/modules.json index 798dcf0d4..aa20e9320 100644 --- a/modules.json +++ b/modules.json @@ -129,7 +129,7 @@ }, "rsem/calculateexpression": { "branch": "master", - "git_sha": "20b042e352fc47ab6dab717a622253e96429e887", + "git_sha": "82cd92d50025a01e1370758ae18fcfe708b6d28c", "installed_by": ["modules"] }, "rsem/preparereference": { @@ -219,7 +219,7 @@ }, "sentieon/rsemcalculateexpression": { "branch": "master", - "git_sha": "2779d18605e9923332155d671f45ed37fa185ff4", + "git_sha": "d9cd3c825e2d05f9c851130100018ae02a766510", "installed_by": ["modules"] }, "sentieon/rsempreparereference": { diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 09f1d1287..b4851805e 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -8,14 +8,14 @@ process RSEM_CALCULATEEXPRESSION { 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' }" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads) // FASTQ files or BAM file for --alignments mode path index output: tuple val(meta), path("*.genes.results") , emit: counts_gene tuple val(meta), path("*.isoforms.results"), emit: counts_transcript tuple val(meta), path("*.stat") , emit: stat - tuple val(meta), path("*.log") , emit: logs + tuple val(meta), path("*.log") , emit: logs, optional:true path "versions.yml" , emit: versions tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star @@ -35,14 +35,34 @@ process RSEM_CALCULATEEXPRESSION { } else if (meta.strandedness == 'reverse') { strandedness = '--strandedness reverse' } - def paired_end = meta.single_end ? "" : "--paired-end" + + // Detect if input is BAM file(s) + def is_bam = reads.toString().toLowerCase().endsWith('.bam') + def alignment_mode = is_bam ? '--alignments' : '' + + // Use metadata for paired-end detection if available, otherwise empty (auto-detect) + def paired_end = meta.containsKey('single_end') ? (meta.single_end ? "" : "--paired-end") : "unknown" + """ INDEX=`find -L ./ -name "*.grp" | sed 's/\\.grp\$//'` + + # Use metadata-based paired-end detection, or auto-detect if no metadata provided + PAIRED_END_FLAG="$paired_end" + if [ "${paired_end}" == "unknown" ]; then + # Auto-detect only if no metadata provided + if [ "${is_bam}" == "true" ]; then + samtools flagstat $reads | grep -q 'paired in sequencing' && PAIRED_END_FLAG="--paired-end" + else + [ ${reads.size()} -gt 1 ] && PAIRED_END_FLAG="--paired-end" + fi + fi + rsem-calculate-expression \\ --num-threads $task.cpus \\ --temporary-folder ./tmp/ \\ + $alignment_mode \\ $strandedness \\ - $paired_end \\ + \$PAIRED_END_FLAG \\ $args \\ $reads \\ \$INDEX \\ @@ -57,12 +77,18 @@ process RSEM_CALCULATEEXPRESSION { stub: prefix = task.ext.prefix ?: "${meta.id}" + def is_bam = reads.toString().toLowerCase().endsWith('.bam') """ touch ${prefix}.genes.results touch ${prefix}.isoforms.results touch ${prefix}.stat touch ${prefix}.log - touch ${prefix}.STAR.genome.bam + + # Only create STAR BAM output when not in alignment mode + if [ "${is_bam}" == "false" ]; then + touch ${prefix}.STAR.genome.bam + fi + touch ${prefix}.genome.bam touch ${prefix}.transcript.bam diff --git a/modules/nf-core/rsem/calculateexpression/meta.yml b/modules/nf-core/rsem/calculateexpression/meta.yml index 0a7fbe1b3..0a7ea6e7d 100644 --- a/modules/nf-core/rsem/calculateexpression/meta.yml +++ b/modules/nf-core/rsem/calculateexpression/meta.yml @@ -21,15 +21,19 @@ input: e.g. [ id:'test', single_end:false ] - reads: type: file - description: Input reads for quantification - pattern: "*.fastq.gz" - - - index: - type: file - description: RSEM index - pattern: "rsem/*" + description: Input reads for quantification (FASTQ files or BAM file for --alignments mode) + pattern: "*.{fastq.gz,bam}" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_2572 # BAM format + - index: + type: file + description: RSEM index + pattern: "rsem/*" + ontologies: [] output: - - counts_gene: - - meta: + counts_gene: + - - meta: type: map description: | Groovy Map containing sample information @@ -38,8 +42,9 @@ output: type: file description: Expression counts on gene level pattern: "*.genes.results" - - counts_transcript: - - meta: + ontologies: [] + counts_transcript: + - - meta: type: map description: | Groovy Map containing sample information @@ -48,8 +53,9 @@ output: type: file description: Expression counts on transcript level pattern: "*.isoforms.results" - - stat: - - meta: + ontologies: [] + stat: + - - meta: type: map description: | Groovy Map containing sample information @@ -58,8 +64,9 @@ output: type: file description: RSEM statistics pattern: "*.stat" - - logs: - - meta: + ontologies: [] + logs: + - - meta: type: map description: | Groovy Map containing sample information @@ -68,13 +75,16 @@ output: type: file description: RSEM logs pattern: "*.log" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam_star: - - meta: + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + bam_star: + - - meta: type: map description: | Groovy Map containing sample information @@ -83,8 +93,9 @@ output: type: file description: BAM file generated by STAR (optional) pattern: "*.STAR.genome.bam" - - bam_genome: - - meta: + ontologies: [] + bam_genome: + - - meta: type: map description: | Groovy Map containing sample information @@ -93,8 +104,9 @@ output: type: file description: Genome BAM file (optional) pattern: "*.genome.bam" - - bam_transcript: - - meta: + ontologies: [] + bam_transcript: + - - meta: type: map description: | Groovy Map containing sample information @@ -103,6 +115,7 @@ output: type: file description: Transcript BAM file (optional) pattern: "*.transcript.bam" + ontologies: [] authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rsem/calculateexpression/tests/alignment.config b/modules/nf-core/rsem/calculateexpression/tests/alignment.config new file mode 100644 index 000000000..8730f1c4b --- /dev/null +++ b/modules/nf-core/rsem/calculateexpression/tests/alignment.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test index 7af876dd8..8860e7df9 100644 --- a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test +++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test @@ -3,9 +3,59 @@ nextflow_process { name "Test Process RSEM_CALCULATEEXPRESSION" script "../main.nf" process "RSEM_CALCULATEEXPRESSION" - config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "rsem" + tag "rsem/calculateexpression" + tag "rsem/preparereference" - test("homo_sapiens") { + + test("homo_sapiens - bam") { + + config "./alignment.config" + + setup { + run("RSEM_PREPAREREFERENCE") { + script "../../../rsem/preparereference/main.nf" + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) + input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', strandedness: 'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/rsem.transcript.bam', checkIfExists: true) + ]) + input[1] = RSEM_PREPAREREFERENCE.out.index + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.counts_gene, + process.out.counts_transcript, + process.out.stat, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - fastq") { + + config "./nextflow.config" setup { run("RSEM_PREPAREREFERENCE") { @@ -39,18 +89,22 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.counts_gene).match("counts_gene") }, - { assert snapshot(process.out.counts_transcript).match("counts_transcript") }, - { assert snapshot(process.out.stat).match("stat") }, - { assert path(process.out.logs.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.counts_gene, + process.out.counts_transcript, + process.out.stat, + process.out.versions + ).match() }, + { assert path(process.out.logs.get(0).get(1)).exists() } ) } } test("homo_sapiens - stub") { - options "-stub" + config "./nextflow.config" + + options "-stub" setup { run("RSEM_PREPAREREFERENCE") { @@ -81,7 +135,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.counts_gene.get(0).get(1)).exists() }, + { assert path(process.out.counts_transcript.get(0).get(1)).exists() }, + { assert path(process.out.stat.get(0).get(1)).exists() }, + { assert path(process.out.logs.get(0).get(1)).exists() }, + { assert snapshot( + process.out.versions + ).match() } ) } } diff --git a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap index 61647071d..1175e2970 100644 --- a/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap +++ b/modules/nf-core/rsem/calculateexpression/tests/main.nf.test.snap @@ -1,6 +1,36 @@ { - "stat": { + "homo_sapiens - stub": { + "content": [ + [ + "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T09:32:28.388711" + }, + "homo_sapiens - fastq": { "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" + ] + ], + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" + ] + ], [ [ { @@ -13,159 +43,28 @@ "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28" ] ] + ], + [ + "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2023-11-22T13:14:18.68683" + "timestamp": "2025-09-12T14:47:20.34162" }, - "homo_sapiens - stub": { + "homo_sapiens - bam": { "content": [ - { - "0": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c" - ], - "5": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_genome": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_star": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "counts_gene": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "counts_transcript": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "logs": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "stat": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c" + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:04:38.064594" - }, - "counts_transcript": { - "content": [ + ], [ [ { @@ -174,42 +73,28 @@ }, "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2023-11-22T13:14:18.682898" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2023-11-22T13:14:18.700958" - }, - "counts_gene": { - "content": [ + ], [ [ { "id": "test", "strandedness": "forward" }, - "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" + [ + "test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4", + "test.model:md5,a7a4bc1734918ef5848604e3362b83e2", + "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28" + ] ] + ], + [ + "versions.yml:md5,823e53afe1ff4f3930ae8392f9f8dd5c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2023-11-22T13:14:18.670998" + "timestamp": "2025-09-15T10:38:32.603705" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/rsemcalculateexpression/main.nf b/modules/nf-core/sentieon/rsemcalculateexpression/main.nf index a7ab3a37c..11d0cbb0f 100644 --- a/modules/nf-core/sentieon/rsemcalculateexpression/main.nf +++ b/modules/nf-core/sentieon/rsemcalculateexpression/main.nf @@ -9,14 +9,14 @@ process SENTIEON_RSEMCALCULATEEXPRESSION { 'community.wave.seqera.io/library/rsem_sentieon:1d3ad86b89bf5cc7' }" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads) // FASTQ files or BAM file for --alignments mode path index output: tuple val(meta), path("*.genes.results") , emit: counts_gene tuple val(meta), path("*.isoforms.results"), emit: counts_transcript tuple val(meta), path("*.stat") , emit: stat - tuple val(meta), path("*.log") , emit: logs + tuple val(meta), path("*.log") , emit: logs, optional:true path "versions.yml" , emit: versions tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star @@ -36,11 +36,18 @@ process SENTIEON_RSEMCALCULATEEXPRESSION { } else if (meta.strandedness == 'reverse') { strandedness = '--strandedness reverse' } - def paired_end = meta.single_end ? "" : "--paired-end" + + // Detect if input is BAM file(s) + def is_bam = reads.toString().toLowerCase().endsWith('.bam') + def alignment_mode = is_bam ? '--alignments' : '' + + // Use metadata for paired-end detection if available, otherwise empty (auto-detect) + def paired_end = meta.containsKey('single_end') ? (meta.single_end ? "" : "--paired-end") : "unknown" def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : "" + """ INDEX=`find -L ./ -name "*.grp" | sed 's/\\.grp\$//'` @@ -48,11 +55,23 @@ process SENTIEON_RSEMCALCULATEEXPRESSION { ln -sf \$(which sentieon) ./STAR export PATH=".:\$PATH" + # Use metadata-based paired-end detection, or auto-detect if no metadata provided + PAIRED_END_FLAG="$paired_end" + if [ "${paired_end}" == "unknown" ]; then + # Auto-detect only if no metadata provided + if [ "${is_bam}" == "true" ]; then + samtools flagstat $reads | grep -q 'paired in sequencing' && PAIRED_END_FLAG="--paired-end" + else + [ ${reads.size()} -gt 1 ] && PAIRED_END_FLAG="--paired-end" + fi + fi + rsem-calculate-expression \\ --num-threads $task.cpus \\ --temporary-folder ./tmp/ \\ + $alignment_mode \\ $strandedness \\ - $paired_end \\ + \$PAIRED_END_FLAG \\ $args \\ $reads \\ \$INDEX \\ @@ -68,12 +87,18 @@ process SENTIEON_RSEMCALCULATEEXPRESSION { stub: prefix = task.ext.prefix ?: "${meta.id}" + def is_bam = reads.toString().toLowerCase().endsWith('.bam') """ touch ${prefix}.genes.results touch ${prefix}.isoforms.results touch ${prefix}.stat touch ${prefix}.log - touch ${prefix}.STAR.genome.bam + + # Only create STAR BAM output when not in alignment mode + if [ "${is_bam}" == "false" ]; then + touch ${prefix}.STAR.genome.bam + fi + touch ${prefix}.genome.bam touch ${prefix}.transcript.bam diff --git a/modules/nf-core/sentieon/rsemcalculateexpression/tests/alignment.config b/modules/nf-core/sentieon/rsemcalculateexpression/tests/alignment.config new file mode 100644 index 000000000..8730f1c4b --- /dev/null +++ b/modules/nf-core/sentieon/rsemcalculateexpression/tests/alignment.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} diff --git a/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test b/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test index 7fb4646a5..e99eaf4c3 100644 --- a/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test +++ b/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test @@ -3,14 +3,59 @@ nextflow_process { name "Test Process SENTIEON_RSEMCALCULATEEXPRESSION" script "../main.nf" process "SENTIEON_RSEMCALCULATEEXPRESSION" - config "./nextflow.config" tag "modules" tag "modules_nfcore" tag "sentieon" tag "sentieon/rsemcalculateexpression" tag "sentieon/rsempreparereference" - test("homo_sapiens") { + + test("homo_sapiens - bam") { + + config "./alignment.config" + + setup { + run("SENTIEON_RSEMPREPAREREFERENCE") { + script "../../../sentieon/rsempreparereference/main.nf" + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) + input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', strandedness: 'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/rsem.transcript.bam', checkIfExists: true) + ]) + input[1] = SENTIEON_RSEMPREPAREREFERENCE.out.index + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.counts_gene, + process.out.counts_transcript, + process.out.stat, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - fastq") { + + config "./nextflow.config" setup { run("SENTIEON_RSEMPREPAREREFERENCE") { @@ -44,18 +89,22 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.counts_gene).match("counts_gene") }, - { assert snapshot(process.out.counts_transcript).match("counts_transcript") }, - { assert snapshot(process.out.stat).match("stat") }, - { assert path(process.out.logs.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.counts_gene, + process.out.counts_transcript, + process.out.stat, + process.out.versions + ).match() }, + { assert path(process.out.logs.get(0).get(1)).exists() } ) } } test("homo_sapiens - stub") { - options "-stub" + config "./nextflow.config" + + options "-stub" setup { run("SENTIEON_RSEMPREPAREREFERENCE") { @@ -86,7 +135,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.counts_gene.get(0).get(1)).exists() }, + { assert path(process.out.counts_transcript.get(0).get(1)).exists() }, + { assert path(process.out.stat.get(0).get(1)).exists() }, + { assert path(process.out.logs.get(0).get(1)).exists() }, + { assert snapshot( + process.out.versions + ).match() } ) } } diff --git a/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test.snap b/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test.snap index f3dee3cc3..539a2b0f5 100644 --- a/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/rsemcalculateexpression/tests/main.nf.test.snap @@ -1,6 +1,36 @@ { - "stat": { + "homo_sapiens - stub": { + "content": [ + [ + "versions.yml:md5,2c37927aa617a24c43688228944f4a96" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T09:32:28.388711" + }, + "homo_sapiens - fastq": { "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" + ] + ], + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" + ] + ], [ [ { @@ -13,159 +43,28 @@ "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28" ] ] + ], + [ + "versions.yml:md5,253b43edb079232ffcdf0b741134cce9" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2023-11-22T13:14:18.68683" + "timestamp": "2025-09-12T14:47:20.34162" }, - "homo_sapiens - stub": { + "homo_sapiens - bam": { "content": [ - { - "0": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,2c37927aa617a24c43688228944f4a96" - ], - "5": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_genome": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_star": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "counts_gene": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "counts_transcript": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "logs": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "stat": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,2c37927aa617a24c43688228944f4a96" + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:04:38.064594" - }, - "counts_transcript": { - "content": [ + ], [ [ { @@ -174,42 +73,28 @@ }, "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2023-11-22T13:14:18.682898" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,253b43edb079232ffcdf0b741134cce9" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2023-11-22T13:14:18.700958" - }, - "counts_gene": { - "content": [ + ], [ [ { "id": "test", "strandedness": "forward" }, - "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" + [ + "test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4", + "test.model:md5,a7a4bc1734918ef5848604e3362b83e2", + "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28" + ] ] + ], + [ + "versions.yml:md5,253b43edb079232ffcdf0b741134cce9" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2023-11-22T13:14:18.670998" + "timestamp": "2025-09-15T10:38:32.603705" } -} +} \ No newline at end of file diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 535f8347a..41626bc7c 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -1,4 +1,4 @@ -def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_align_args) { +def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_align_args, quantifier = 'salmon') { def argsToMap = { String args -> args.split(/\s(?=--)/).collectEntries { def parts = it.trim().split(/\s+/, 2) @@ -6,27 +6,50 @@ def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_alig } } + // Common args between pipeline and RSEM def base_args = """ --quantMode TranscriptomeSAM - --twopassMode Basic --outSAMtype BAM Unsorted - --readFilesCommand zcat - --runRNGseed 0 - --outFilterMultimapNmax 20 - --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD - --outSAMstrandField intronMotif + --readFilesCommand zcat """.trim() + // Add quantifier-specific args + if (quantifier == 'rsem') { + // RSEM-compatible configuration + base_args += " " + """ + --outSAMunmapped Within + --outFilterType BySJout + --outFilterMultimapNmax 20 + --outFilterMismatchNmax 999 + --outFilterMismatchNoverLmax 0.04 + --alignIntronMin 20 + --alignIntronMax 1000000 + --alignMatesGapMax 1000000 + --alignSJoverhangMin 8 + --alignSJDBoverhangMin 1 + --sjdbScore 1 + """.trim() + } else { + // Standard pipeline configuration + base_args += " " + """ + --twopassMode Basic + --runRNGseed 0 + --outFilterMultimapNmax 20 + --alignSJDBoverhangMin 1 + --outSAMstrandField intronMotif + """.trim() + } + if (save_unaligned || contaminant_screening) { - base_args += "\n--outReadsUnmapped Fastx" + base_args += " --outReadsUnmapped Fastx" } def final_args_map = argsToMap(base_args) + (extra_star_align_args ? argsToMap(extra_star_align_args) : [:]) final_args_map.collect { key, value -> "${key} ${value}".trim() }.join(' ') } -if (!params.skip_alignment && params.aligner == 'star_salmon') { +if (!params.skip_alignment && (params.aligner == 'star_salmon' || params.aligner == 'star_rsem')) { process { // We have to condition this, because the args are slightly different between the latest STAR and the one compatible with iGenomes @@ -34,19 +57,31 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { withName: '.*:ALIGN_STAR:STAR_ALIGN' { ext.args = { + def quantifier = params.aligner == 'star_rsem' ? 'rsem' : 'salmon' + def extra_args = params.extra_star_align_args ?: '' + if (quantifier == 'salmon') { + extra_args += ' --quantTranscriptomeSAMoutput BanSingleEnd' + } generateStarAlignArgs( params.save_unaligned, params.contaminant_screening, - (params.extra_star_align_args ?: '') + ' --quantTranscriptomeSAMoutput BanSingleEnd' + extra_args, + quantifier ) } } withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES|.*:ALIGN_STAR:SENTIEON_STAR_ALIGN' { ext.args = { + def quantifier = params.aligner == 'star_rsem' ? 'rsem' : 'salmon' + def extra_args = params.extra_star_align_args ?: '' + if (quantifier == 'salmon') { + extra_args += ' --quantTranscriptomeBan Singleend' + } generateStarAlignArgs( params.save_unaligned, params.contaminant_screening, - (params.extra_star_align_args ?: '') + ' --quantTranscriptomeBan Singleend' + extra_args, + quantifier ) } } diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 559f6846d..20db3067c 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -214,7 +214,7 @@ workflow PREPARE_GENOME { def prepare_tool_indices = [] if (!skip_bbsplit) { prepare_tool_indices << 'bbsplit' } if (!skip_sortmerna) { prepare_tool_indices << 'sortmerna' } - if (!skip_alignment && aligner) { prepare_tool_indices << aligner } + if ((!skip_alignment && aligner) || aligner == 'star_rsem') { prepare_tool_indices << aligner } if (!skip_pseudo_alignment && pseudo_aligner) { prepare_tool_indices << pseudo_aligner } //--------------------------------------------------------- @@ -288,7 +288,7 @@ workflow PREPARE_GENOME { // 11) STAR index (e.g. for 'star_salmon') -> needs FASTA if built //---------------------------------------------------- ch_star_index = Channel.empty() - if ('star_salmon' in prepare_tool_indices) { + if (prepare_tool_indices.intersect(['star_salmon', 'star_rsem'])) { if (star_index) { if (star_index.endsWith('.tar.gz')) { ch_star_index = UNTAR_STAR_INDEX ([ [:], file(star_index, checkIfExists: true) ]).untar.map { it[1] } diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config index f09e17f04..ee8545b94 100644 --- a/subworkflows/local/prepare_genome/nextflow.config +++ b/subworkflows/local/prepare_genome/nextflow.config @@ -59,7 +59,6 @@ process { } withName: '.*RSEM_PREPAREREFERENCE_GENOME' { - ext.args = '--star' publishDir = [ path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/quantify_rsem/main.nf b/subworkflows/local/quantify_rsem/main.nf index 33a271a6e..db5628136 100644 --- a/subworkflows/local/quantify_rsem/main.nf +++ b/subworkflows/local/quantify_rsem/main.nf @@ -4,14 +4,12 @@ include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression' include { RSEM_MERGE_COUNTS } from '../../../modules/local/rsem_merge_counts' -include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools' include { SENTIEON_RSEMCALCULATEEXPRESSION } from '../../../modules/nf-core/sentieon/rsemcalculateexpression' workflow QUANTIFY_RSEM { take: - reads // channel: [ val(meta), [ reads ] ] - index // channel: /path/to/rsem/index/ - fasta // channel: [ val(meta), [ fasta ] ] + reads // channel: [ val(meta), [ reads ] ] - FASTQ or BAM files + index // channel: /path/to/rsem/index/ use_sentieon_star // boolean: determines whether RSEM is run with Sentieon accelerated STAR main: @@ -30,21 +28,12 @@ workflow QUANTIFY_RSEM { ch_rsem_out = RSEM_CALCULATEEXPRESSION } - ch_bam_star = ch_rsem_out.out.bam_star ch_counts_gene = ch_rsem_out.out.counts_gene ch_counts_transcript = ch_rsem_out.out.counts_transcript ch_stat = ch_rsem_out.out.stat ch_logs = ch_rsem_out.out.logs - ch_bam_genome = ch_rsem_out.out.bam_genome - ch_bam_transcript = ch_rsem_out.out.bam_transcript ch_versions = ch_versions.mix(ch_rsem_out.out.versions.first()) - // - // Sort, index BAM file and run samtools stats, flagstat and idxstats - // - BAM_SORT_STATS_SAMTOOLS ( ch_bam_star, fasta ) - ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) - // // Merge counts across samples // @@ -55,20 +44,10 @@ workflow QUANTIFY_RSEM { ch_versions = ch_versions.mix(RSEM_MERGE_COUNTS.out.versions) emit: - counts_gene = ch_counts_gene // channel: [ val(meta), counts ] - counts_transcript = ch_counts_transcript // channel: [ val(meta), counts ] - stat = ch_stat // channel: [ val(meta), stat ] - logs = ch_logs // channel: [ val(meta), logs ] - bam_star = ch_bam_star // channel: [ val(meta), bam ] - bam_genome = ch_bam_genome // channel: [ val(meta), bam ] - bam_transcript = ch_bam_transcript // channel: [ val(meta), bam ] - - bam = BAM_SORT_STATS_SAMTOOLS.out.bam // channel: [ val(meta), [ bam ] ] - bai = BAM_SORT_STATS_SAMTOOLS.out.bai // channel: [ val(meta), [ bai ] ] - csi = BAM_SORT_STATS_SAMTOOLS.out.csi // channel: [ val(meta), [ csi ] ] - stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + counts_gene = ch_counts_gene // channel: [ val(meta), counts ] + counts_transcript = ch_counts_transcript // channel: [ val(meta), counts ] + stat = ch_stat // channel: [ val(meta), stat ] + logs = ch_logs // channel: [ val(meta), logs ] merged_counts_gene = RSEM_MERGE_COUNTS.out.counts_gene // path: *.gene_counts.tsv merged_tpm_gene = RSEM_MERGE_COUNTS.out.tpm_gene // path: *.gene_tpm.tsv diff --git a/subworkflows/local/quantify_rsem/nextflow.config b/subworkflows/local/quantify_rsem/nextflow.config index ec4ba6750..0ade162ae 100644 --- a/subworkflows/local/quantify_rsem/nextflow.config +++ b/subworkflows/local/quantify_rsem/nextflow.config @@ -2,9 +2,6 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') { process { withName: '.*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION|.*:QUANTIFY_RSEM:SENTIEON_RSEMCALCULATEEXPRESSION' { ext.args = [ - '--star', - '--star-output-genome-bam', - '--star-gzipped-read-file', '--estimate-rspd', '--seed 1' ].join(' ').trim() @@ -14,12 +11,6 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') { mode: params.publish_dir_mode, pattern: "*.{stat,results}" ], - [ - path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir }, - mode: params.publish_dir_mode, - pattern: "*.bam", - saveAs: { params.save_align_intermeds ? it : null } - ], [ path: { "${params.outdir}/${params.aligner}/log" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test b/subworkflows/local/quantify_rsem/tests/main.nf.test index 04485a00e..270c6c3fe 100644 --- a/subworkflows/local/quantify_rsem/tests/main.nf.test +++ b/subworkflows/local/quantify_rsem/tests/main.nf.test @@ -26,14 +26,10 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', strandedness: 'forward' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + 'genomics/homo_sapiens/illumina/bam/rsem.transcript.bam', checkIfExists: true) ]) input[1] = RSEM_PREPAREREFERENCE.out.index - input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) - input[3] = use_sentieon_star + input[2] = use_sentieon_star """ } } @@ -42,81 +38,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - file(workflow.out.logs[0][1]).name, workflow.out.counts_gene, workflow.out.counts_transcript, workflow.out.stat, - workflow.out.bam_star, - workflow.out.bam_genome, - workflow.out.bam_transcript, - workflow.out.counts_transcript, - workflow.out.bam, - workflow.out.bai, - workflow.out.csi, - workflow.out.stats, - workflow.out.flagstat, - workflow.out.idxstats, - workflow.out.merged_counts_gene, - workflow.out.merged_tpm_gene, - workflow.out.merged_counts_transcript, - workflow.out.merged_tpm_transcript, - workflow.out.versions - ).match()} - ) - } - } - - test("homo_sapiens - sentieon") { - tag "sentieon" - setup { - run("SENTIEON_RSEMPREPAREREFERENCE") { - script "../../../../modules/nf-core/sentieon/rsempreparereference/main.nf" - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) - input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true)) - """ - } - } - } - - when { - workflow { - """ - use_sentieon_star = true - - input[0] = Channel.of([ - [ id:'test', strandedness: 'forward' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] - ]) - input[1] = SENTIEON_RSEMPREPAREREFERENCE.out.index - input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) - input[3] = use_sentieon_star - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - file(workflow.out.logs[0][1]).name, - workflow.out.counts_gene, - workflow.out.counts_transcript, - workflow.out.stat, - workflow.out.bam_star, - workflow.out.bam_genome, - workflow.out.bam_transcript, - workflow.out.counts_transcript, - workflow.out.bam, - workflow.out.bai, - workflow.out.csi, - workflow.out.stats, - workflow.out.flagstat, - workflow.out.idxstats, workflow.out.merged_counts_gene, workflow.out.merged_tpm_gene, workflow.out.merged_counts_transcript, @@ -150,14 +74,10 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', strandedness: 'forward' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + 'genomics/homo_sapiens/illumina/bam/rsem.transcript.bam', checkIfExists: true) ]) input[1] = RSEM_PREPAREREFERENCE.out.index - input[2] = Channel.of([[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) - input[3] = use_sentieon_star + input[2] = use_sentieon_star """ } } @@ -193,14 +113,10 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', strandedness: 'forward' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + 'genomics/homo_sapiens/illumina/bam/rsem.transcript.bam', checkIfExists: true) ]) input[1] = SENTIEON_RSEMPREPAREREFERENCE.out.index - input[2] = Channel.of([[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) - input[3] = use_sentieon_star + input[2] = use_sentieon_star """ } } diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap index 5dd451bdf..d58f6edff 100644 --- a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap +++ b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "homo_sapiens - stub": { + "homo_sapiens - sentieon - stub": { "content": [ { "0": [ @@ -20,54 +20,6 @@ "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "10": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "11": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "12": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "13": [ - "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "14": [ - "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "15": [ - "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "16": [ - "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "17": [ - "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", - "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", - "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", - "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c", - "versions.yml:md5,f151349bd7086cb08134496033e78cea", - "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" - ], "2": [ [ { @@ -87,97 +39,20 @@ ] ], "4": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "5": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "6": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "7": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "8": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "9": [ - - ], - "bai": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_genome": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_star": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", + "versions.yml:md5,773c15c4ecb7d486a4bdd8ef73e7ac5d" ], "counts_gene": [ [ @@ -197,27 +72,6 @@ "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], "logs": [ [ { @@ -248,33 +102,19 @@ "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "stats": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], "versions": [ - "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", - "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", - "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c", - "versions.yml:md5,f151349bd7086cb08134496033e78cea", - "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" + "versions.yml:md5,773c15c4ecb7d486a4bdd8ef73e7ac5d" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-10-21T14:49:44.270456428" + "timestamp": "2025-09-15T16:59:19.581004" }, - "homo_sapiens - sentieon - stub": { + "homo_sapiens - stub": { "content": [ { "0": [ @@ -295,54 +135,6 @@ "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "10": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "11": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "12": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "13": [ - "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "14": [ - "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "15": [ - "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "16": [ - "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "17": [ - "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", - "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", - "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", - "versions.yml:md5,773c15c4ecb7d486a4bdd8ef73e7ac5d", - "versions.yml:md5,f151349bd7086cb08134496033e78cea", - "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" - ], "2": [ [ { @@ -362,97 +154,20 @@ ] ], "4": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "5": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "6": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "7": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "8": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "9": [ - - ], - "bai": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_genome": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_star": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.STAR.genome.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", + "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c" ], "counts_gene": [ [ @@ -472,27 +187,6 @@ "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], "logs": [ [ { @@ -523,35 +217,20 @@ "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "stats": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], "versions": [ - "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", - "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", - "versions.yml:md5,773c15c4ecb7d486a4bdd8ef73e7ac5d", - "versions.yml:md5,f151349bd7086cb08134496033e78cea", - "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" + "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-10-21T14:49:44.270456428" + "timestamp": "2025-09-15T16:56:01.229068" }, "homo_sapiens": { "content": [ - "test.log", [ [ { @@ -582,48 +261,6 @@ "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28" ] ] - ], - [ - - ], - [ - - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,e8a05da15bb08d3a333be637fdd8be58" - ] - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" - ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - ], [ "rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1" @@ -642,109 +279,10 @@ "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-03T19:53:14.561568" - }, - "homo_sapiens - sentieon": { - "content": [ - "test.log", - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.genes.results:md5,c7ec226f76736ea805771e73553ae359" - ] - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" - ] - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - [ - "test.cnt:md5,76249e6b2f3c104f414aae596ba2c2f4", - "test.model:md5,a7a4bc1734918ef5848604e3362b83e2", - "test.theta:md5,de2e4490c98cc5383a86ae8225fd0a28" - ] - ] - ], - [ - - ], - [ - - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcript.bam:md5,e8a05da15bb08d3a333be637fdd8be58" - ] - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.isoforms.results:md5,99f7f80aa505b44ca429fdebbd7dd5d8" - ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - "rsem.merged.gene_counts.tsv:md5,f3b586000c97c89aec45360772e73df1" - ], - [ - "rsem.merged.gene_tpm.tsv:md5,e6ae3dfa9913a7c15b705ec27c376212" - ], - [ - "rsem.merged.transcript_counts.tsv:md5,235c002b811360183494a2aac74d1f5b" - ], - [ - "rsem.merged.transcript_tpm.tsv:md5,d38f22667e3b8012f1d783b8d5159ccc" - ], - [ - "versions.yml:md5,12a2fefc07645c553dd331e91bb21cce", - "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9" - ] - ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.04.3" }, - "timestamp": "2025-08-12T07:52:13.10736278" + "timestamp": "2025-09-16T08:19:00.078928064" } } \ No newline at end of file diff --git a/subworkflows/local/quantify_rsem/tests/nextflow.config b/subworkflows/local/quantify_rsem/tests/nextflow.config index 4b2da69ca..6318bc5a8 100644 --- a/subworkflows/local/quantify_rsem/tests/nextflow.config +++ b/subworkflows/local/quantify_rsem/tests/nextflow.config @@ -1,16 +1,3 @@ -process { - - // Needs the glob to force the config to be applied - withName: ".*RSEM_PREPAREREFERENCE|.*SENTIEON_RSEMPREPAREREFERENCE" { - ext.args = "--star " - } - - withName: ".*RSEM_CALCULATEEXPRESSION|.*SENTIEON_RSEMCALCULATEEXPRESSION" { - ext.args = '--star --star-gzipped-read-file' - } - -} - // NOTE This is how pipeline users will use Sentieon in real world use if (System.getenv('SENTIEON_LICSRVR_IP')) { env.SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" diff --git a/tests/.nftignore b/tests/.nftignore index 532d75bae..2013f8551 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -13,7 +13,7 @@ sortmerna/*.sortmerna.log star_rsem/*.stat/*.{cnt,model,theta} star_rsem/*.{genes,isoforms}.results star_rsem/log/*.log -star_salmon/log/*.Log.{final.out,out,progress.out} +star_{salmon,rsem}/log/*.Log.{final.out,out,progress.out} trimgalore/*fastq.gz_trimming_report.txt umitools/*.umi_extract.log {hisat2,star_rsem,star_salmon}/*.{bam,bam.bai} diff --git a/tests/bam_input.nf.test b/tests/bam_input.nf.test index 57b19ee92..2a2db041e 100644 --- a/tests/bam_input.nf.test +++ b/tests/bam_input.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" - test("BAM input") { + test("BAM input for Salmon") { when { params { @@ -34,4 +34,36 @@ nextflow_pipeline { ) } } + + test("BAM input for RSEM") { + + when { + params { + input = "https://raw.githubusercontent.com/nf-core/test-datasets/470a36d464328a152153da94971dd1a73dfe2d05/samplesheet/v3.10/samplesheet_test_with_rsem_bams.csv" + outdir = "$outputDir" + skip_alignment = true + aligner = 'star_rsem' + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) + removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } } diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 310579cca..17dfec744 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,7 +1,7 @@ { - "BAM input": { + "BAM input for Salmon": { "content": [ - 129, + 139, { "BBMAP_BBSPLIT": { "bbmap": 39.18 @@ -15,6 +15,13 @@ "CUSTOM_GETCHROMSIZES": { "getchromsizes": 1.21 }, + "CUSTOM_TX2GENE": { + "python": "3.10.4" + }, + "DESEQ2_QC_STAR_SALMON": { + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" + }, "DUPRADAR": { "bioconductor-dupradar": "1.32.0" }, @@ -60,6 +67,9 @@ "RSEQC_READDUPLICATION": { "rseqc": "5.0.2" }, + "SALMON_QUANT": { + "salmon": "1.10.3" + }, "SAMTOOLS_FLAGSTAT": { "samtools": 1.21 }, @@ -72,12 +82,21 @@ "SAMTOOLS_STATS": { "samtools": 1.21 }, + "SE_GENE_UNIFIED": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "SE_TRANSCRIPT_UNIFIED": { + "bioconductor-summarizedexperiment": "1.32.0" + }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { "subread": "2.0.6" }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, "UCSC_BEDCLIP": { "ucsc": 377 }, @@ -117,6 +136,8 @@ "multiqc/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/multiqc_report_data/multiqc_software_versions.txt", "multiqc/multiqc_report_data/multiqc_sources.txt", + "multiqc/multiqc_report_data/multiqc_star_salmon_deseq2_clustering.txt", + "multiqc/multiqc_report_data/multiqc_star_salmon_deseq2_pca.txt", "multiqc/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", "multiqc/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", "multiqc/multiqc_report_data/picard_MeanQualityByCycle_histogram_1.txt", @@ -185,6 +206,8 @@ "multiqc/multiqc_report_plots/pdf/samtools-stats-dp.pdf", "multiqc/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/multiqc_report_plots/pdf/star_salmon_deseq2_clustering.pdf", + "multiqc/multiqc_report_plots/pdf/star_salmon_deseq2_pca.pdf", "multiqc/multiqc_report_plots/png", "multiqc/multiqc_report_plots/png/dupradar.png", "multiqc/multiqc_report_plots/png/fail_strand_check_table.png", @@ -221,6 +244,8 @@ "multiqc/multiqc_report_plots/png/samtools-stats-dp.png", "multiqc/multiqc_report_plots/png/samtools_alignment_plot-cnt.png", "multiqc/multiqc_report_plots/png/samtools_alignment_plot-pct.png", + "multiqc/multiqc_report_plots/png/star_salmon_deseq2_clustering.png", + "multiqc/multiqc_report_plots/png/star_salmon_deseq2_pca.png", "multiqc/multiqc_report_plots/svg", "multiqc/multiqc_report_plots/svg/dupradar.svg", "multiqc/multiqc_report_plots/svg/fail_strand_check_table.svg", @@ -257,6 +282,8 @@ "multiqc/multiqc_report_plots/svg/samtools-stats-dp.svg", "multiqc/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/multiqc_report_plots/svg/star_salmon_deseq2_clustering.svg", + "multiqc/multiqc_report_plots/svg/star_salmon_deseq2_pca.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "samtools", @@ -266,16 +293,91 @@ "samtools/WT_REP1.sorted.bam.bai", "samtools/WT_REP2.sorted.bam.bai", "star_salmon", + "star_salmon/RAP1_IAA_30M_REP1", "star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam", "star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "star_salmon/RAP1_IAA_30M_REP1/aux_info", + "star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv", + "star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz", + "star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz", + "star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json", + "star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz", + "star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz", + "star_salmon/RAP1_IAA_30M_REP1/cmd_info.json", + "star_salmon/RAP1_IAA_30M_REP1/libParams", + "star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt", + "star_salmon/RAP1_IAA_30M_REP1/logs", + "star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log", + "star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf", + "star_salmon/RAP1_IAA_30M_REP1/quant.sf", + "star_salmon/RAP1_UNINDUCED_REP1", "star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam", "star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz", + "star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz", + "star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json", + "star_salmon/RAP1_UNINDUCED_REP1/libParams", + "star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt", + "star_salmon/RAP1_UNINDUCED_REP1/logs", + "star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log", + "star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf", + "star_salmon/RAP1_UNINDUCED_REP1/quant.sf", + "star_salmon/RAP1_UNINDUCED_REP2", "star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam", "star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz", + "star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz", + "star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json", + "star_salmon/RAP1_UNINDUCED_REP2/libParams", + "star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt", + "star_salmon/RAP1_UNINDUCED_REP2/logs", + "star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log", + "star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf", + "star_salmon/RAP1_UNINDUCED_REP2/quant.sf", + "star_salmon/WT_REP1", "star_salmon/WT_REP1.markdup.sorted.bam", "star_salmon/WT_REP1.markdup.sorted.bam.bai", + "star_salmon/WT_REP1/aux_info", + "star_salmon/WT_REP1/aux_info/ambig_info.tsv", + "star_salmon/WT_REP1/aux_info/expected_bias.gz", + "star_salmon/WT_REP1/aux_info/fld.gz", + "star_salmon/WT_REP1/aux_info/meta_info.json", + "star_salmon/WT_REP1/aux_info/observed_bias.gz", + "star_salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "star_salmon/WT_REP1/cmd_info.json", + "star_salmon/WT_REP1/libParams", + "star_salmon/WT_REP1/libParams/flenDist.txt", + "star_salmon/WT_REP1/logs", + "star_salmon/WT_REP1/logs/salmon_quant.log", + "star_salmon/WT_REP1/quant.genes.sf", + "star_salmon/WT_REP1/quant.sf", + "star_salmon/WT_REP2", "star_salmon/WT_REP2.markdup.sorted.bam", "star_salmon/WT_REP2.markdup.sorted.bam.bai", + "star_salmon/WT_REP2/aux_info", + "star_salmon/WT_REP2/aux_info/ambig_info.tsv", + "star_salmon/WT_REP2/aux_info/expected_bias.gz", + "star_salmon/WT_REP2/aux_info/fld.gz", + "star_salmon/WT_REP2/aux_info/meta_info.json", + "star_salmon/WT_REP2/aux_info/observed_bias.gz", + "star_salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "star_salmon/WT_REP2/cmd_info.json", + "star_salmon/WT_REP2/libParams", + "star_salmon/WT_REP2/libParams/flenDist.txt", + "star_salmon/WT_REP2/logs", + "star_salmon/WT_REP2/logs/salmon_quant.log", + "star_salmon/WT_REP2/quant.genes.sf", + "star_salmon/WT_REP2/quant.sf", "star_salmon/bigwig", "star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig", "star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig", @@ -287,6 +389,19 @@ "star_salmon/bigwig/WT_REP1.reverse.bigWig", "star_salmon/bigwig/WT_REP2.forward.bigWig", "star_salmon/bigwig/WT_REP2.reverse.bigWig", + "star_salmon/deseq2_qc", + "star_salmon/deseq2_qc/R_sessionInfo.log", + "star_salmon/deseq2_qc/deseq2.dds.RData", + "star_salmon/deseq2_qc/deseq2.pca.vals.txt", + "star_salmon/deseq2_qc/deseq2.plots.pdf", + "star_salmon/deseq2_qc/deseq2.sample.dists.txt", + "star_salmon/deseq2_qc/size_factors", + "star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt", + "star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt", + "star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt", + "star_salmon/deseq2_qc/size_factors/WT_REP1.txt", + "star_salmon/deseq2_qc/size_factors/WT_REP2.txt", + "star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData", "star_salmon/dupradar", "star_salmon/dupradar/box_plot", "star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", @@ -652,6 +767,16 @@ "star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls", "star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls", "star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls", + "star_salmon/salmon.merged.gene.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", "star_salmon/samtools_stats", "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", @@ -713,7 +838,8 @@ "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", "star_salmon/stringtie/WT_REP2.coverage.gtf", "star_salmon/stringtie/WT_REP2.gene.abundance.txt", - "star_salmon/stringtie/WT_REP2.transcripts.gtf" + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -736,6 +862,31 @@ "RAP1_UNINDUCED_REP2.sorted.bam.bai:md5,6e2ed96bd496e98bce89c4d69c31db5d", "WT_REP1.sorted.bam.bai:md5,687b540b3b69b826968a2fb4a16e5609", "WT_REP2.sorted.bam.bai:md5,fe846da56caf2cafb72d11a6070895e1", + "ambig_info.tsv:md5,604c0c31a357c82178a3308315da30a2", + 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"star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_rsem/stringtie", + "star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + 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"WT_REP2.featureCounts.tsv:md5,da2c6d621864e2f26958e2c299708c3e", + "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2", + "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", + "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", + "coverage_profile_along_genes_(high).txt:md5,60a3cace1ababb161a8f048a4684d421", + "coverage_profile_along_genes_(low).txt:md5,0f3c3aa4e32495bc2fe323ca3b9b6dd5", + "coverage_profile_along_genes_(total).txt:md5,0f3c3aa4e32495bc2fe323ca3b9b6dd5", + "coverage_profile_along_genes_(high).txt:md5,125b9b3d568aa7b394c1f5b005a828ef", + "coverage_profile_along_genes_(low).txt:md5,8a63efdae22d5cb9bd4b1404020c2956", + "coverage_profile_along_genes_(total).txt:md5,8a63efdae22d5cb9bd4b1404020c2956", + "coverage_profile_along_genes_(high).txt:md5,4dc80c27b5e8dabe5022c1d0609b111b", + "coverage_profile_along_genes_(low).txt:md5,b7058ee3f437638f5cf567c54a2baf29", + "coverage_profile_along_genes_(total).txt:md5,b7058ee3f437638f5cf567c54a2baf29", + "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", + "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", + "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", + "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de", + "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,a2a8e31dbd0ebd0c12f3f968ffd5391b", + "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,9ec058d3a4162fd1b4c6175e2106eef4", + "WT_REP1.infer_experiment.txt:md5,d55921c0084806cdf49b9bd8653c8e09", + "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,5dfd0678eefe33f2c45eea45f6262557", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,19a438db88bdb92228e64a0a8350adbd", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,fd95c815882005ccd312821bb9cf3dc7", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,addcf0f6836e0f81184d5ddaa525895f", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,4aa066edadef5325777dd54ca042cfab", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,84d39323e429ad397223542b9d6f7c40", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,74b66ee626c2864ece15c4872224856c", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,daedcbf428f3912587722da1c5db50d1", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,49e5912dedb709344c7a14b5980c1b40", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,7e81ace0a68bfe42482420b7275de195" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-09-09T19:13:13.065436646" + "timestamp": "2025-09-15T20:20:27.355744216" } } \ No newline at end of file diff --git a/tests/sentieon_star_rsem.nf.test b/tests/sentieon_star_rsem.nf.test deleted file mode 100644 index 65571e31b..000000000 --- a/tests/sentieon_star_rsem.nf.test +++ /dev/null @@ -1,70 +0,0 @@ -nextflow_pipeline { - - name "Test pipeline with STAR aligner and RSEM for quantification" - script "../main.nf" - tag "pipeline" - - test("Params: --aligner star_rsem --use_sentieon_star") { - - when { - params { - outdir = "$outputDir" - aligner = 'star_rsem' - use_sentieon_star = true - } - } - - then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assertAll( - { assert workflow.success}, - { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), - // All stable path name, with a relative path - stable_name, - // All files with stable contents - stable_path - ).match() } - ) - } - } - - test("Params: --aligner star_rsem --use_sentieon_star - stub") { - - options "-stub" - - when { - params { - outdir = "$outputDir" - aligner = 'star_rsem' - use_sentieon_star = true - } - } - - then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assertAll( - { assert workflow.success}, - { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), - // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key) - removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"), - // All stable path name, with a relative path - stable_name, - // All files with stable contents - stable_path - ).match() } - ) - } - } -} diff --git a/tests/sentieon_star_rsem.nf.test.snap b/tests/sentieon_star_rsem.nf.test.snap deleted file mode 100644 index 1ba04bfaf..000000000 --- a/tests/sentieon_star_rsem.nf.test.snap +++ /dev/null @@ -1,1398 +0,0 @@ -{ - "Params: --aligner star_rsem --use_sentieon_star": { - "content": [ - 201, - { - "BBMAP_BBSPLIT": { - "bbmap": 39.18 - }, - "BEDTOOLS_GENOMECOV_FW": { - "bedtools": "2.31.1" - }, - "CAT_FASTQ": { - "cat": 9.5 - }, - "CUSTOM_CATADDITIONALFASTA": { - "python": "3.12.2" - }, - "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.21 - 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"coverage_profile_along_genes_(total).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00", - "coverage_profile_along_genes_(high).txt:md5,cdb2c00c43121e3beccd7f670b34e05e", - "coverage_profile_along_genes_(low).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed", - "coverage_profile_along_genes_(total).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed", - "coverage_profile_along_genes_(high).txt:md5,70c95fbc100f14911d2cc348bdff1587", - "coverage_profile_along_genes_(low).txt:md5,86e56ef794277bcf1e0d121a088b8581", - "coverage_profile_along_genes_(total).txt:md5,86e56ef794277bcf1e0d121a088b8581", - "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", - "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", - "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", - "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", - "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", - "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", - "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", - "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de", - "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,a2a8e31dbd0ebd0c12f3f968ffd5391b", - "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,9ec058d3a4162fd1b4c6175e2106eef4", - "WT_REP1.infer_experiment.txt:md5,d55921c0084806cdf49b9bd8653c8e09", - "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,5dfd0678eefe33f2c45eea45f6262557", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,19a438db88bdb92228e64a0a8350adbd", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,a02dec82f07185700cc237e617ecc809", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,addcf0f6836e0f81184d5ddaa525895f", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,5354c397909a72a25607c550170e2874", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,389b41d0123509f18af9da9bb2e626cd", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,282685569dc501a8769c98c0c2885378", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,daedcbf428f3912587722da1c5db50d1", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,49e5912dedb709344c7a14b5980c1b40", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,7e81ace0a68bfe42482420b7275de195" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-12T12:46:35.67191347" - }, - "Params: --aligner star_rsem --use_sentieon_star - stub": { - "content": [ - 27, - { - "BBMAP_BBSPLIT": { - "bbmap": 39.18 - }, - "CAT_FASTQ": { - "cat": 9.5 - }, - "CUSTOM_CATADDITIONALFASTA": { - "python": null - }, - "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.21 - }, - "FASTQC": { - "fastqc": "0.12.1" - }, - "FQ_LINT": { - "fq": "0.12.0 (2024-07-08)" - }, - "GTF2BED": { - "perl": "5.26.2" - }, - "GTF_FILTER": { - "python": "3.9.5" - }, - "GUNZIP_ADDITIONAL_FASTA": { - "gunzip": 1.13 - }, - "GUNZIP_GTF": { - "gunzip": 1.13 - }, - "TRIMGALORE": { - "cutadapt": 4.9, - "pigz": 2.8, - "trimgalore": "0.6.10" - }, - "UNTAR_RSEM_INDEX": { - "untar": 1.34 - }, - "UNTAR_SALMON_INDEX": { - "untar": 1.34 - } - }, - [ - "custom", - "custom/out", - "custom/out/genome_transcriptome.fasta", - "custom/out/genome_transcriptome.gtf", - "fastqc", - "fastqc/raw", - "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", - "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", - "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", - "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", - "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", - "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", - "fastqc/raw/WT_REP1_raw.html", - "fastqc/raw/WT_REP1_raw.zip", - "fastqc/raw/WT_REP2_raw.html", - "fastqc/raw/WT_REP2_raw.zip", - "fastqc/trim", - "fq_lint", - "fq_lint/raw", - "fq_lint/raw/RAP1_IAA_30M_REP1.fq_lint.txt", - "fq_lint/raw/RAP1_UNINDUCED_REP1.fq_lint.txt", - "fq_lint/raw/RAP1_UNINDUCED_REP2.fq_lint.txt", - "fq_lint/raw/WT_REP1.fq_lint.txt", - "fq_lint/raw/WT_REP2.fq_lint.txt", - "multiqc", - "multiqc/star_rsem", - "multiqc/star_rsem/multiqc_data", - "multiqc/star_rsem/multiqc_plots", - "multiqc/star_rsem/multiqc_report.html", - "pipeline_info", - "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", - "trimgalore", - "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" - ], - [ - "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.2" - }, - "timestamp": "2025-06-03T20:30:37.383920745" - } -} diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 9accc3292..f0f78f74f 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1,7 +1,7 @@ { "Params: --aligner star_rsem": { "content": [ - 201, + 207, { "BBMAP_BBSPLIT": { "bbmap": 39.18 @@ -69,6 +69,10 @@ "RSEM_MERGE_COUNTS": { "sed": 4.7 }, + "RSEM_PREPAREREFERENCE_GENOME": { + "rsem": "1.3.1", + "star": "2.7.10a" + }, "RSEQC_BAMSTAT": { "rseqc": "5.0.2" }, @@ -114,6 +118,16 @@ "SE_TRANSCRIPT_UNIFIED": { "bioconductor-summarizedexperiment": "1.32.0" }, + "STAR_ALIGN": { + "gawk": "5.1.0", + "samtools": 1.21, + "star": "2.7.11b" + }, + "STAR_GENOMEGENERATE": { + "gawk": "5.1.0", + "samtools": 1.21, + "star": "2.7.11b" + }, "STRINGTIE_STRINGTIE": { "stringtie": "2.2.3" }, @@ -134,9 +148,6 @@ "UCSC_BEDGRAPHTOBIGWIG": { "ucsc": 469 }, - "UNTAR_RSEM_INDEX": { - "untar": 1.34 - }, "UNTAR_SALMON_INDEX": { "untar": 1.34 } @@ -263,6 +274,7 @@ "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_star.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca.txt", "multiqc/star_rsem/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", @@ -299,6 +311,8 @@ "multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "multiqc/star_rsem/multiqc_report_data/samtools-stats-dp.txt", "multiqc/star_rsem/multiqc_report_data/samtools_alignment_plot.txt", + "multiqc/star_rsem/multiqc_report_data/star_alignment_plot.txt", + "multiqc/star_rsem/multiqc_report_data/star_summary_table.txt", "multiqc/star_rsem/multiqc_report_plots", "multiqc/star_rsem/multiqc_report_plots/pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", @@ -370,8 +384,11 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_rsem/multiqc_report_plots/png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", @@ -442,8 +459,11 @@ "multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png", + "multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-cnt.png", + "multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering.png", "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca.png", + "multiqc/star_rsem/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_rsem/multiqc_report_plots/svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", @@ -514,8 +534,11 @@ "multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering.svg", "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "salmon", @@ -741,11 +764,26 @@ "star_rsem/featurecounts/WT_REP2.featureCounts.tsv", "star_rsem/featurecounts/WT_REP2.featureCounts.tsv.summary", "star_rsem/log", - "star_rsem/log/RAP1_IAA_30M_REP1.log", - "star_rsem/log/RAP1_UNINDUCED_REP1.log", - "star_rsem/log/RAP1_UNINDUCED_REP2.log", - "star_rsem/log/WT_REP1.log", - "star_rsem/log/WT_REP2.log", + "star_rsem/log/RAP1_IAA_30M_REP1.Log.final.out", + "star_rsem/log/RAP1_IAA_30M_REP1.Log.out", + "star_rsem/log/RAP1_IAA_30M_REP1.Log.progress.out", + "star_rsem/log/RAP1_IAA_30M_REP1.SJ.out.tab", + "star_rsem/log/RAP1_UNINDUCED_REP1.Log.final.out", + "star_rsem/log/RAP1_UNINDUCED_REP1.Log.out", + "star_rsem/log/RAP1_UNINDUCED_REP1.Log.progress.out", + "star_rsem/log/RAP1_UNINDUCED_REP1.SJ.out.tab", + "star_rsem/log/RAP1_UNINDUCED_REP2.Log.final.out", + "star_rsem/log/RAP1_UNINDUCED_REP2.Log.out", + "star_rsem/log/RAP1_UNINDUCED_REP2.Log.progress.out", + "star_rsem/log/RAP1_UNINDUCED_REP2.SJ.out.tab", + "star_rsem/log/WT_REP1.Log.final.out", + "star_rsem/log/WT_REP1.Log.out", + "star_rsem/log/WT_REP1.Log.progress.out", + "star_rsem/log/WT_REP1.SJ.out.tab", + "star_rsem/log/WT_REP2.Log.final.out", + "star_rsem/log/WT_REP2.Log.out", + "star_rsem/log/WT_REP2.Log.progress.out", + "star_rsem/log/WT_REP2.SJ.out.tab", "star_rsem/picard_metrics", "star_rsem/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "star_rsem/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -1176,7 +1214,7 @@ "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", - "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", + "multiqc_citations.txt:md5,eb19d85c883385624d8310f517901b7e", "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", @@ -1243,6 +1281,11 @@ "WT_REP2.biotype_counts_mqc.tsv:md5,c04c2936bbfac3bff284f96b7233b158", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.tsv:md5,da2c6d621864e2f26958e2c299708c3e", + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,0a2ccd13ce40c6007cf24568f13af9b4", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,275bbb2009c43d411fbbbd6636b5e9bc", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1eb030549d877ab7fa51fe1d632ffe09", + "WT_REP1.SJ.out.tab:md5,5292020e46d35c14354f13696bbf0ab0", + "WT_REP2.SJ.out.tab:md5,3fab08b47b8b3cab91ae91dec8750152", "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2", "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", @@ -1258,10 +1301,10 @@ "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", - "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", - "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", - "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", - "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", + "rsem.merged.gene_counts.tsv:md5,990cdaf5071c9bfd3d2d99296feb68f3", + "rsem.merged.gene_tpm.tsv:md5,349f2184161d6b269a0f5c4da1dee07a", + "rsem.merged.transcript_counts.tsv:md5,3ca2bb5c22438e0bd104c9d052bc8241", + "rsem.merged.transcript_tpm.tsv:md5,f59e35398f30d49875e41bcc03d082ed", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,a2a8e31dbd0ebd0c12f3f968ffd5391b", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,9ec058d3a4162fd1b4c6175e2106eef4", @@ -1291,13 +1334,13 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nextflow": "25.04.3" }, - "timestamp": "2025-08-12T12:46:35.67191347" + "timestamp": "2025-09-15T20:52:56.262347961" }, "Params: --aligner star_rsem - stub": { "content": [ - 27, + 28, { "BBMAP_BBSPLIT": { "bbmap": 39.18 @@ -1329,14 +1372,20 @@ "GUNZIP_GTF": { "gunzip": 1.13 }, + "RSEM_PREPAREREFERENCE_GENOME": { + "rsem": "1.3.1", + "star": "2.7.10a" + }, + "STAR_GENOMEGENERATE": { + "gawk": "5.1.0", + "samtools": 1.21, + "star": "2.7.11b" + }, "TRIMGALORE": { "cutadapt": 4.9, "pigz": 2.8, "trimgalore": "0.6.10" }, - "UNTAR_RSEM_INDEX": { - "untar": 1.34 - }, "UNTAR_SALMON_INDEX": { "untar": 1.34 } @@ -1390,8 +1439,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-06-03T20:30:37.383920745" + "timestamp": "2025-09-15T17:52:54.558516396" } -} +} \ No newline at end of file diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 08a26416b..d3a3ded0c 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -125,7 +125,7 @@ workflow RNASEQ { } .branch { meta, reads, genome_bam, transcriptome_bam -> - bam: genome_bam || transcriptome_bam + bam: params.skip_alignment && (genome_bam || transcriptome_bam) return [ meta, genome_bam, transcriptome_bam ] fastq: reads.size() > 0 && reads[0] return [ meta.findAll {it.key != 'percent_mapped'}, reads ] @@ -203,7 +203,7 @@ workflow RNASEQ { ch_star_log = Channel.empty() ch_unaligned_sequences = Channel.empty() - if (!params.skip_alignment && params.aligner == 'star_salmon') { + if (!params.skip_alignment && (params.aligner == 'star_salmon' || params.aligner == 'star_rsem')) { // Check if an AWS iGenome has been provided to use the appropriate version of STAR def is_aws_igenome = false if (params.fasta && params.gtf) { @@ -267,6 +267,30 @@ workflow RNASEQ { .mix(ALIGN_STAR.out.flagstat.collect{it[1]}) .mix(ALIGN_STAR.out.idxstats.collect{it[1]}) } + } + + if (params.aligner == 'star_rsem') { + + QUANTIFY_RSEM ( + ch_transcriptome_bam, + ch_rsem_index, + params.use_sentieon_star + ) + ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.stat.collect{it[1]}) + ch_versions = ch_versions.mix(QUANTIFY_RSEM.out.versions) + + if (!params.skip_qc & !params.skip_deseq2_qc) { + DESEQ2_QC_RSEM ( + QUANTIFY_RSEM.out.merged_counts_gene, + ch_pca_header_multiqc, + ch_clustering_header_multiqc + ) + ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_RSEM.out.pca_multiqc.collect()) + ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_RSEM.out.dists_multiqc.collect()) + ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions) + } + + } else if (params.aligner == 'star_salmon') { // // SUBWORKFLOW: Count reads from BAM alignments using Salmon @@ -299,41 +323,6 @@ workflow RNASEQ { } } - // - // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with RSEM - // - if (!params.skip_alignment && params.aligner == 'star_rsem') { - QUANTIFY_RSEM ( - ch_strand_inferred_filtered_fastq, - ch_rsem_index, - ch_fasta.map { [ [:], it ] }, - params.use_sentieon_star - ) - ch_genome_bam = ch_genome_bam.mix(QUANTIFY_RSEM.out.bam) - ch_transcriptome_bam = ch_transcriptome_bam.mix(QUANTIFY_RSEM.out.bam_transcript) - ch_unprocessed_bams = ch_genome_bam.join(ch_transcriptome_bam) - ch_genome_bam_index = ch_genome_bam_index.mix(params.bam_csi_index ? QUANTIFY_RSEM.out.csi : QUANTIFY_RSEM.out.bai) - ch_star_log = QUANTIFY_RSEM.out.logs - ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.stats.collect{it[1]}) - ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.flagstat.collect{it[1]}) - ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.idxstats.collect{it[1]}) - ch_multiqc_files = ch_multiqc_files.mix(ch_star_log.collect{it[1]}) - ch_multiqc_files = ch_multiqc_files.mix(QUANTIFY_RSEM.out.stat.collect{it[1]}) - - ch_versions = ch_versions.mix(QUANTIFY_RSEM.out.versions) - - if (!params.skip_qc & !params.skip_deseq2_qc) { - DESEQ2_QC_RSEM ( - QUANTIFY_RSEM.out.merged_counts_gene, - ch_pca_header_multiqc, - ch_clustering_header_multiqc - ) - ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_RSEM.out.pca_multiqc.collect()) - ch_multiqc_files = ch_multiqc_files.mix(DESEQ2_QC_RSEM.out.dists_multiqc.collect()) - ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions) - } - } - // // SUBWORKFLOW: Alignment with HISAT2 //