Merge pull request #111 from sanger-tol/busco_tmp

Busco tmp
sanger-tol · Sep 13, 2024 · ca10b9b · ca10b9b
2 parents 18d2daf + 5a581b1
commit ca10b9b
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Showing 8 changed files with 37 additions and 3 deletions.
diff --git a/.github/workflows/sanger_test.yml b/.github/workflows/sanger_test.yml
@@ -23,6 +23,7 @@ jobs:
           parameters: |
             {
               "outdir": "${{ secrets.TOWER_WORKDIR_PARENT }}/results/${{ github.repository }}/results-${{ env.REVISION }}",
+              "use_work_dir_as_temp": true,
             }
           profiles: test,sanger,singularity,cleanup
       - uses: actions/upload-artifact@v3

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## – Bellsprout – []
+## [[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 The pipeline has now been validated for draft (unpublished) assemblies.
 
@@ -17,6 +17,7 @@ The pipeline has now been validated for draft (unpublished) assemblies.
   for the original Yaml configuration files of the Snakemake version.
 - New option `--skip_taxon_filtering` to skip the taxon filtering in blast searches.
   Mostly relevant for draft assemblies.
+- Introduced the `--use_work_dir_as_temp` parameter to avoid leaving files in `/tmp`.
 
 ### Parameters
 
@@ -25,6 +26,7 @@ The pipeline has now been validated for draft (unpublished) assemblies.
 | --yaml        |                        |
 |               | --busco_lineages       |
 |               | --skip_taxon_filtering |
+|               | --use_work_dir_as_temp |
 
 > **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.
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -81,7 +81,8 @@ process {
     }
 
     withName: "BUSCO" {
-        scratch = true
+        // Obey "use_work_dir_as_temp", except for large genomes
+        scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) }
         ext.args = { 'test' in workflow.profile.tokenize(',') ?
                         // Additional configuration to speed processes up during testing.
                         // Note: BUSCO *must* see the double-quotes around the parameters

diff --git a/conf/test.config b/conf/test.config
@@ -35,4 +35,7 @@ params {
     blastp  = "${projectDir}/assets/test/mMelMel3.1.buscogenes.dmnd"
     blastx  = "${projectDir}/assets/test/mMelMel3.1.buscoregions.dmnd"
     blastn  = "${projectDir}/assets/test/nt_mMelMel3.1"
+
+    // Need to be set to avoid overfilling /tmp
+    use_work_dir_as_temp = true
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -30,4 +30,7 @@ params {
     blastp  = "${projectDir}/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd"
     blastx  = "${projectDir}/assets/test_full/gfLaeSulp1.1.buscoregions.dmnd"
     blastn  = "${projectDir}/assets/test_full/nt_gfLaeSulp1.1"
+
+    // Need to be set to avoid overfilling /tmp
+    use_work_dir_as_temp = true
 }
diff --git a/conf/test_raw.config b/conf/test_raw.config
@@ -36,4 +36,7 @@ params {
     blastp  = "${projectDir}/assets/test/mMelMel3.1.buscogenes.dmnd"
     blastx  = "${projectDir}/assets/test/mMelMel3.1.buscoregions.dmnd"
     blastn  = "${projectDir}/assets/test/nt_mMelMel3.1/"
+
+    // Need to be set to avoid overfilling /tmp
+    use_work_dir_as_temp = true
 }
diff --git a/nextflow.config b/nextflow.config
@@ -35,6 +35,9 @@ params {
     blastn                     = null
     skip_taxon_filtering       = false
 
+    // Execution options
+    use_work_dir_as_temp        = false
+
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -246,7 +249,7 @@ manifest {
     description     = """Quality assessment of genome assemblies"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.6.0-dev'
+    version         = '0.6.0'
     doi             = '10.5281/zenodo.7949058'
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -148,6 +148,21 @@
                 }
             }
         },
+        "execution": {
+            "title": "Execution",
+            "type": "object",
+            "description": "Control the execution of the pipeline.",
+            "default": "",
+            "properties": {
+                "use_work_dir_as_temp": {
+                    "type": "boolean",
+                    "description": "Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.",
+                    "fa_icon": "fas fa-arrow-circle-down",
+                    "hidden": true
+                }
+            },
+            "fa_icon": "fas fa-running"
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -353,6 +368,9 @@
         {
             "$ref": "#/definitions/databases"
         },
+        {
+            "$ref": "#/definitions/execution"
+        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },