precom busco documentation

Author: tkchafin

.github/workflows/ci.yml

@@ -41,3 +41,10 @@ jobs:
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+      - name: Run pipeline with test data and precomputed BUSCOs
+        # You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nobusco,docker --outdir ./results

CHANGELOG.md

@@ -14,6 +14,7 @@ The pipeline is now considered to be a complete and suitable replacement for the
 - Updated the Blastn settings to allow 7 days runtime at most, since that
   covers 99.7% of the jobs.
 - Allow database inputs to be optionally compressed (`.tar.gz`)
+- Allow `BUSCO` run outputs to be optionally pre-computed and provided with `--busco_output`
 
 ### Software dependencies
 
@@ -27,6 +28,14 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | multiqc     | 1.20 and 1.21     | 1.20 and 1.25.1 |
 | samtools    | 1.18 and 1.19.2   | 1.20 and 1.21   |
 
+### Parameters
+
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+|               | --busco-output         |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ## [[0.6.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.6.0)] – Bellsprout – [2024-09-13]
 
 The pipeline has now been validated for draft (unpublished) assemblies.

conf/test_nobusco.config

@@ -37,8 +37,10 @@ params {
     blastn  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/nt_mMelMel3.1.tar.gz"
 
     // Precomputed BUSCO outputs
-    // Note we deliberately left out archaea_odb10 to test the addition of missing lineages
-    busco_output = "busco_output"
+    // busco_output_noArchaea.tar.gz deliberately leaves out archaea_odb10 to test the pipeline's detection and filling of missing lineages
+    // Switch to *_busco_output.tar.gz for fully precomputed BUSCOs
+    busco_output = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/GCA_922984935.2_busco_output_noArchaea.tar.gz"
+    //busco_output = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/GCA_922984935.2_busco_output.tar.gz"
 
     // Need to be set to avoid overfilling /tmp
     use_work_dir_as_temp = true

docs/usage.md

@@ -54,6 +54,24 @@ An [example samplesheet](assets/test/samplesheet.csv) has been provided with the
 The pipeline can also accept a samplesheet generated by the [nf-core/fetchngs](https://nf-co.re/fetchngs) pipeline (tested with version 1.11.0).
 The pipeline then needs the `--fetchngs_samplesheet true` option _and_ `--align true`, since the data files would all be unaligned.
 
+### Support for pre-computed `BUSCO` outputs
+
+The pipeline may be optionally run with a set of pre-computed [`BUSCO`](https://busco.ezlab.org) runs, provided using the `--busco_output` parameter. These can be provided as either a directory path, or a `.tar.gz` compressed archive. The contents should be each `run_` output directory (directly from `BUSCO`) named as `run_[odb_dabasase_name]`:
+
+```
+GCA_922984935.2_busco_output/
+├── run_archaea_odb10
+├── run_bacteria_odb10
+├── run_carnivora_odb10
+├── run_eukaryota_odb10
+├── run_eutheria_odb10
+├── run_laurasiatheria_odb10
+├── run_mammalia_odb10
+├── run_metazoa_odb10
+├── run_tetrapoda_odb10
+└── run_vertebrata_odb10
+```
+
 ## Database parameters
 
 Configure access to your local databases with the `--busco`, `--blastp`, `--blastx`, `--blastn`, and `--taxdump` parameters.