Fix #746

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#746](https://github.com/nf-core/rnaseq/issues/746)] - Add `tin.py` output to MultiQC report
 - Expose additional arguments to UMI-tools as pipeline params: `--umitools_bc_pattern2` is required if the UMI is located on read 2. `--umitools_umi_separator` will often be needed in conjunction with `--skip_umi_extract` as most other tools such as Illumina's `BCL Convert` use a colon instead of an underscore to separate the UMIs. The `--umitools_grouping_method` allows to fine-tune handling of similar but non-identical UMIs.
 - Updated pipeline template to [nf-core/tools 2.5.1](https://github.com/nf-core/tools/releases/tag/2.5.1)
 
@@ -18,6 +19,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 |               | `--umitools_umi_separator`   |
 |               | `--umitools_grouping_method` |
 
+### Software dependencies
+
+Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `multiqc`   | 1.11        | 1.13        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+> **NB:** Dependency has been **added** if just the new version information is present.
+> **NB:** Dependency has been **removed** if version information isn't present.
+
 ## [[3.8.1](https://github.com/nf-core/rnaseq/releases/tag/3.8.1)] - 2022-05-27
 
 - [[#834](https://github.com/nf-core/rnaseq/issues/834)] - `nf-core download` fails with version 3.8 of the pipeline

assets/multiqc_config.yml

@@ -104,7 +104,7 @@ sp:
   rseqc/infer_experiment:
     fn: "*.infer_experiment.txt"
   rseqc/tin:
-    fn: "*.tin.txt"
+    fn: "*.summary.txt"
 
   picard/markdups:
     fn: "*.MarkDuplicates.metrics.txt"

modules/local/multiqc.nf

@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path multiqc_config