Update for btk plots

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Restructured locations and names of output files, see [output.md](/docs/output.md)
 - The `sample` samplesheet column can now contain `/` to organise the `read_mapping/` outputs in sub-directories.
 - Added parameter `--window_size` to partition sequences and calculate per-window statistics
+- Updated `blobtk/images` to `blobtk/plots` (an nf-core module)
 
 ### Parameters
 
@@ -27,7 +28,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | Dependency | Old version   | New version     |
 | ---------- | ------------- | --------------- |
 | blast      | 2.15.0        | 2.17.0          |
-| blobtk     | 0.5.1         | 0.7.1           |
+| blobtk     | 0.5.1         | 0.8.0           |
 | diamond    | 2.1.16        | 2.1.23          |
 | gunzip     | 1.1           | 1.13            |
 | minimap2   | 2.28          | 2.29            |

conf/base.config

@@ -118,6 +118,7 @@ process {
         memory = { 1.GB * Math.pow(4, task.attempt) }
         time   = { 1.h * Math.pow(8, task.attempt) }
     }
+
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
         accelerator = { workflow.profile.contains('gpu') ? 1 : null }

conf/modules.config

@@ -126,6 +126,7 @@ process {
         ext.args = { "--evalue 1.0e-25  --max-target-seqs 10 --max-hsps 1" + ( params.use_work_dir_as_temp ? " --tmpdir ./blastx_tmp/" : "" ) }
     }
 
+
     withName: "BLOBTK_DEPTH" {
         ext.args = "-s ${ params.window_size }"
         publishDir = [
@@ -182,11 +183,13 @@ process {
         ]
     }
 
-    withName: "BLOBTK_IMAGES" {
+    withName: "BLOBTK_PLOT" {
         publishDir = [
             path: { "${params.outdir}/blobtoolkit/plots" },
             mode: params.publish_dir_mode,
         ]
+        ext.args    = { "--scale-factor 0.6 ${extra_args.args}" }
+        ext.prefix  = { "${meta.id}.${extra_args.name}" }
     }
 
     withName: "JSONIFY_TAXDUMP" {

modules.json

@@ -13,7 +13,12 @@
                     },
                     "blobtk/depth": {
                         "branch": "master",
-                        "git_sha": "f0ee15907fcece823c1cd5129902405d36108191",
+                        "git_sha": "afe7137ce04ae44c379341ae8223c65ea579c300",
+                        "installed_by": ["modules"]
+                    },
+                    "blobtk/plot": {
+                        "branch": "master",
+                        "git_sha": "afe7137ce04ae44c379341ae8223c65ea579c300",
                         "installed_by": ["modules"]
                     },
                     "busco/busco": {

modules/local/blobtoolkit/createblobdir.nf

@@ -1,5 +1,5 @@
 process BLOBTOOLKIT_CREATEBLOBDIR {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     container "docker.io/genomehubs/blobtoolkit:4.4.6"