Merge pull request #1128 from wm75/artic-ivar-pangolin-update

Update ivar-based SARS-CoV-2 wf with latest pangolin changes

Author: mvdbeek

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/CHANGELOG.md

@@ -1,5 +1,34 @@
 # Changelog
 
+## [0.4] - 2026-03-04
+
+### Changed
+
+The pangolin lineage assignment step will no longer use the latest pangolin-data version downloaded from the web at workflow run time (this feature has been removed from the latest version of the pangolin Galaxy tool).
+Instead users can now select a pangolin-data version from the ones cached on their Galaxy server, or they can choose to go with the version of pangolin-data provided by the pangolin Galaxy wrapper (currently, this is v1.37 of pangolin-data).
+
+### Updated tools
+
+- `toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3.4+galaxy3`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0`.
+
+  With this tool update fastp gets executed with the --dont_eval_duplication
+  option, i.e. the fastp report will no longer contain the duplicate estimate
+  for the raw reads.
+  An estimate of duplicated reads based on mapping results is still available
+  as part of the "QC reports for mapping results" workflow output.
+
+- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.4+galaxy1`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.4.4+galaxy0`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.4+galaxy0`.
+- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0`.
+- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0`.
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3`.
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3`.
+
 ## [0.3.1] - 2025-04-28
 
 ### Added

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/README.md

@@ -7,7 +7,12 @@ This workflow is also the subject of a Galaxy Training Network tutorial (current
 It differs from [this workflow](https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling) in
 that it does not use `lofreq` and is aimed at rapid analysis of majority variants and lineage/clade assignment with `pangolin` and `nextclade`.
 
+Note:
+The version of nextclade used in this workflow is rather outdated.
+For up-to-date nextclade assignments consider analyzing the Combined Consensus Genomes output at https://clades.nextstrain.org/.
+
 TODO:
 
-1. Add support for QC using negative and positive controls
-2. Integrate with phylogeny tools including IQTree and UShER (and possibly more).
+1. Get nextclade on Galaxy updated and use it here.
+2. Add support for QC using negative and positive controls.
+3. Integrate with phylogeny tools including IQTree and UShER (and possibly more).

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis-test.yml

@@ -36,6 +36,7 @@
           hashes:
           - hash_function: SHA-1
             hash_value: 52890d3130f8e2bdc83bd6f9186f433f438bbd52
+    Version of pangolin-data to use: null
   outputs:
     all_samples_nextclade:
       asserts:
@@ -47,6 +48,11 @@
       asserts:
         has_text_matching:
           expression: "taxon\tlineage\tconflict\tambiguity_score\tscorpio_call\tscorpio_support\tscorpio_conflict\tscorpio_notes\tversion\tpangolin_version\tscorpio_version\tconstellation_version\tis_designated\tqc_status\tqc_notes\tnote"
+        has_text:
+          # Attention when updating this check:
+          # The input param "Version of pangolin-data to use" mentions the default version in its annotation string.
+          # When the bundled version changes in a newer version of pangolin causing this check to fail, you need to also update the param annotation.
+          text: "PANGO-v1.37"
     combined_multifasta:
       asserts:
         has_line: