Tweak to only use BAM files with --skip_alignment

Author: pinin4fjords

docs/output.md

@@ -11,7 +11,7 @@ nextflow run nf-core/rnaseq -profile test_full,<docker/singularity/institute>
 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
@@ -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.
 
 </details>
 

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
 
@@ -156,9 +156,11 @@ SAMPLE2,/path/sample2_R1.fastq.gz,,reverse,results/star_salmon/SAMPLE2.sorted.ba
 
 **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.

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 ]