Use a TrueType font for plotting sequence names with last/dotplot. (#…

…7404) * Use a TrueType font for plotting sequence names with `last/dotplot`. The `last-dotplot` command normally picks scalable fonts by default but did not manage to do so on the conda install in the images. Therefore I hardcode the path (which is likely to change when the images are updated). Not using a scalable font prevents users from changing the font size using the command-line argument `-s` of `last-dotplot`. In addition, I found that the CI tests did not check the outputted images, and corrected that too in this commit. * Pin pillow version and query conda for its base directory. Thanks: Leon Hafner * Avoid unbound variable error, thanks to ChatGPT * Try a different way to find pillow's TrueType font in conda. * Fix typo * Try finding a font in the open-fonts package. * Desperate attempt to pull the information * Bingo! * Unpin pillow
nf-core · Feb 3, 2025 · ea8c309 · ea8c309
1 parent 256a6dd
commit ea8c309
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Showing 4 changed files with 105 additions and 23 deletions.
diff --git a/modules/nf-core/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml
@@ -4,3 +4,4 @@ channels:
 
 dependencies:
   - bioconda::last=1608
+  - conda-forge::open-fonts=0.7.0
diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf
@@ -4,8 +4,8 @@ process LAST_DOTPLOT {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data'
-        : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a35d17772276115874eda45f17b05407c9855ecec8c11d39cce49f0028f44cfb/data'
+        : 'community.wave.seqera.io/library/last_open-fonts:f1048938520a62ad'}"
 
     input:
     tuple val(meta), path(maf), path(annot_b)
@@ -26,7 +26,10 @@ process LAST_DOTPLOT {
     def annot_a_arg = annot_a ? "-a ${annot_a}" : ''
     def annot_b_arg = annot_b ? "-b ${annot_b}" : ''
     """
+    TTF=/home/ubuntu/conda_pkgs_dir/open-fonts-0.7.0-1/fonts/open-fonts/DejaVuSansMono-Regular.ttf
+    [ -e "\$TTF" ] || TTF="/opt/conda/fonts/open-fonts/DejaVuSansMono-Regular.ttf"
     last-dotplot \\
+        -f \$TTF \\
         $args \\
         $annot_a_arg \\
         $annot_b_arg \\

diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test b/modules/nf-core/last/dotplot/tests/main.nf.test
@@ -32,8 +32,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert process.out.png.get(0).get(1).endsWith("test.png") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -58,8 +57,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert process.out.gif.get(0).get(1).endsWith("test.gif") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -85,8 +83,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match() },
-                { assert process.out.png.get(0).get(1).endsWith("test.png") }
+                { assert snapshot(process.out).match() }
             )
         }
 

diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test.snap b/modules/nf-core/last/dotplot/tests/main.nf.test.snap
@@ -1,38 +1,119 @@
 {
     "sarscov2 - contigs - genome - gif": {
         "content": [
-            [
-                "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gif:md5,cec730f1d060a82553cefe2311708bad"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
+                ],
+                "gif": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gif:md5,cec730f1d060a82553cefe2311708bad"
+                    ]
+                ],
+                "png": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-21T09:18:32.629314"
+        "timestamp": "2025-02-03T09:27:56.241408"
     },
     "sarscov2 - contigs - genome - png - stub": {
         "content": [
-            [
-                "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
-            ]
+            {
+                "0": [
+
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
+                ],
+                "gif": [
+
+                ],
+                "png": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-21T09:18:48.084683"
+        "timestamp": "2025-01-31T09:55:40.665796"
     },
     "sarscov2 - contigs - genome - png": {
         "content": [
-            [
-                "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
-            ]
+            {
+                "0": [
+
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.png:md5,005267881455bdab7c8bd87ec27060f8"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
+                ],
+                "gif": [
+
+                ],
+                "png": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.png:md5,005267881455bdab7c8bd87ec27060f8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-21T09:18:17.971205"
+        "timestamp": "2025-02-03T09:27:41.83809"
     }
 }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4,3 +4,4 @@ channels:

		dependencies:
		- bioconda::last=1608
		- conda-forge::open-fonts=0.7.0