Update tools: MultiQC and BBSplit

.gitignore

@@ -14,3 +14,5 @@ test-datasets/
 test.tap
 test.xml
 .vscode/mcp.json
+modules/nf-core/**/tests/
+subworkflows/nf-core/**/tests/

CHANGELOG.md

@@ -11,16 +11,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [2073](https://github.com/nf-core/sarek/pull/2073) - Update MultiQC to version 1.33
+
 ### Fixed
 
 - [2069](https://github.com/nf-core/sarek/pull/2069) - Propagate tbi indices for HaplotypeCaller and Haplotyper to fix bug with merging vcfs and tbis.
+- [2073](https://github.com/nf-core/sarek/pull/2073) - Apply fix for BBSplit error: `unterminated s' command`
 
 ### Removed
 
 ### Dependencies
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| multiqc    | 1.31        | 1.32        |
 
 ### Parameters
 

assets/multiqc_config.yml

@@ -22,6 +22,7 @@ run_modules:
   - custom_content
   - fastqc
   - fastp
+  - bbmap
   - picard
   - samtools
   - mosdepth
@@ -38,6 +39,8 @@ module_order:
         - "*_val_*.zip"
   - fastp:
       name: "FastP (Read preprocessing)"
+  - bbmap:
+      name: "BBsplit (Reference genome binning)"
   - picard:
       name: "GATK4 MarkDuplicates"
       info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)."

modules.json

@@ -12,7 +12,7 @@
                     },
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "6da7216c83d9d885bdeb7aef1bcb9b51a90f370b",
+                        "git_sha": "2ddc92b750c7553f7a7becb4982851cef3ab848e",
                         "installed_by": ["modules"]
                     },
                     "bcftools/annotate": {
@@ -388,7 +388,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
                         "installed_by": ["modules"]
                     },
                     "muse/call": {

subworkflows/local/fastq_preprocess_gatk/main.nf

@@ -150,6 +150,8 @@ workflow FASTQ_PREPROCESS_GATK {
                                     )
                                     .primary_fastq
 
+            reports = reports.mix(BBMAP_BBSPLIT.out.stats.collect{ _meta, stats -> stats })
+
             versions = versions.mix(BBMAP_BBSPLIT.out.versions.first())
 
         } else {

tests/.nftignore

@@ -2,6 +2,8 @@
 annotation/**/*.vcf.{gz,gz.tbi}
 csv/*.csv
 multiqc/multiqc_data/bcftools*.txt
+multiqc/multiqc_data/bbmap*.txt
+multiqc/multiqc_data/bbsplit_stats_table.txt
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
 multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt
 multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt

tests/bbsplit.nf.test.snap

@@ -65,6 +65,9 @@
                 "csv/variantcalled.csv",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/bbmap-bbsplit_plot.txt",
+                "multiqc/multiqc_data/bbmap.txt",
+                "multiqc/multiqc_data/bbsplit_stats_table.txt",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_adapter_content_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -107,6 +110,9 @@
                 "multiqc/multiqc_data/vcftools_tstv_by_qual.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
+                "multiqc/multiqc_plots/pdf/bbmap-bbsplit_plot-cnt.pdf",
+                "multiqc/multiqc_plots/pdf/bbmap-bbsplit_plot-pct.pdf",
+                "multiqc/multiqc_plots/pdf/bbsplit_stats_table.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
@@ -131,6 +137,9 @@
                 "multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf",
                 "multiqc/multiqc_plots/pdf/vcftools_tstv_by_count.pdf",
                 "multiqc/multiqc_plots/png",
+                "multiqc/multiqc_plots/png/bbmap-bbsplit_plot-cnt.png",
+                "multiqc/multiqc_plots/png/bbmap-bbsplit_plot-pct.png",
+                "multiqc/multiqc_plots/png/bbsplit_stats_table.png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
@@ -155,6 +164,9 @@
                 "multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png",
                 "multiqc/multiqc_plots/png/vcftools_tstv_by_count.png",
                 "multiqc/multiqc_plots/svg",
+                "multiqc/multiqc_plots/svg/bbmap-bbsplit_plot-cnt.svg",
+                "multiqc/multiqc_plots/svg/bbmap-bbsplit_plot-pct.svg",
+                "multiqc/multiqc_plots/svg/bbsplit_stats_table.svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",