Simplified hybridization

GallVp · Jul 21, 2024 · db7fb04 · db7fb04
1 parent 3cc883c
commit db7fb04
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Showing 16 changed files with 16 additions and 10 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -80,7 +80,7 @@ jobs:
           head: ${{ github.sha }}
           base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
           n_parents: 2
-          ignored: "nf-core-modules/*"
+          ignored: "nf-core-modules/modules/nf-core/**"
 
       - name: Separate modules and subworkflows
         id: outputs
@@ -90,6 +90,7 @@ jobs:
 
       - name: debug
         run: |
+          echo ${{ steps.list.outputs.components }}
           echo ${{ steps.outputs.outputs.modules }}
           echo ${{ steps.outputs.outputs.subworkflows }}
 

diff --git a/README.md b/README.md
@@ -40,7 +40,7 @@ And [more...](./SUBMITTED.md)
 
 Hybrid sub-workflows are not supported by nf-core/tools. See: https://github.com/nf-core/tools/issues/1927
 
-The workaround is to install nf-core modules in the nf-core-modules which is setup as a dummy pipeline. The nf-core modules needed for testing are then symlinked to `modules/nf-core` and the nf-core modules needed for sub-workflows are symlinked to `modules/gallvp`. See: [nf-core-hybridisation.sh](./nf-core-hybridisation.sh)
+The workaround is to install nf-core modules in the nf-core-modules which is setup as a dummy pipeline. The nf-core modules needed for sub-workflows are copied to `modules/gallvp`. See: [nf-core-hybridisation.sh](./nf-core-hybridisation.sh)
 
 ## References
 

diff --git a/docs/AVAILABLE.txt b/docs/AVAILABLE.txt
@@ -5,6 +5,7 @@
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrretriever/lai">modules/gallvp/ltrretriever/lai</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrharvest">modules/gallvp/ltrharvest</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/ltrfinder">modules/gallvp/ltrfinder</a></li>
+<li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/gunzip">modules/gallvp/gunzip</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/custom/shortenfastaids">modules/gallvp/custom/shortenfastaids</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/custom/restoregffids">modules/gallvp/custom/restoregffids</a></li>
 <li><a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/annosine">modules/gallvp/annosine</a></li>
diff --git a/docs/index.html b/docs/index.html
@@ -124,6 +124,11 @@ <h1>gallvp/nxf-components</h1>
                     >modules/gallvp/ltrfinder</a
                 >
             </li>
+            <li>
+                <a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/gunzip"
+                    >modules/gallvp/gunzip</a
+                >
+            </li>
             <li>
                 <a href="https://github.com/gallvp/nxf-components/tree/main/modules/gallvp/custom/shortenfastaids"
                     >modules/gallvp/custom/shortenfastaids</a

diff --git a/modules/nf-core/gunzip/environment.yml → modules/gallvp/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml → modules/gallvp/gunzip/environment.yml
diff --git a/modules/nf-core/gunzip/main.nf → modules/gallvp/gunzip/main.nf b/modules/nf-core/gunzip/main.nf → modules/gallvp/gunzip/main.nf
diff --git a/modules/nf-core/gunzip/meta.yml → modules/gallvp/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml → modules/gallvp/gunzip/meta.yml
diff --git a/modules/nf-core/gunzip/tests/main.nf.test → modules/gallvp/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test → modules/gallvp/gunzip/tests/main.nf.test
@@ -4,7 +4,7 @@ nextflow_process {
     script "../main.nf"
     process "GUNZIP"
     tag "gunzip"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "modules"
 
     test("Should run without failures") {

diff --git a/...es/nf-core/gunzip/tests/main.nf.test.snap → ...les/gallvp/gunzip/tests/main.nf.test.snap b/...es/nf-core/gunzip/tests/main.nf.test.snap → ...les/gallvp/gunzip/tests/main.nf.test.snap
diff --git a/modules/nf-core/gunzip/tests/nextflow.config → modules/gallvp/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config → modules/gallvp/gunzip/tests/nextflow.config
diff --git a/modules/nf-core/gunzip/tests/tags.yml → modules/gallvp/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml → modules/gallvp/gunzip/tests/tags.yml
diff --git a/modules/gallvp/ltrfinder/tests/main.nf.test b/modules/gallvp/ltrfinder/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "LTRFINDER"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "ltrfinder"
     tag "gunzip/main"
 

diff --git a/modules/gallvp/ltrharvest/tests/main.nf.test b/modules/gallvp/ltrharvest/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "LTRHARVEST"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "ltrharvest"
 
     test("homo_sapiens - genome_21_fasta") {

diff --git a/modules/gallvp/ltrretriever/lai/tests/main.nf.test b/modules/gallvp/ltrretriever/lai/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     config "./nextflow.config"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "gunzip"
     tag "ltrretriever"
     tag "ltrretriever/ltrretriever"

diff --git a/modules/gallvp/ltrretriever/ltrretriever/tests/main.nf.test b/modules/gallvp/ltrretriever/ltrretriever/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     config "./nextflow.config"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "ltrretriever"
     tag "ltrretriever/ltrretriever"
     tag "gunzip/main"

diff --git a/nf-core-hybridisation.sh b/nf-core-hybridisation.sh
@@ -3,12 +3,11 @@
 cp_hybrid_module() {
     mkdir -p "./modules/gallvp/$1"
     cp -r "./nf-core-modules/modules/nf-core/$1/"* "./modules/gallvp/$1"
+    sed -i 's/modules_nfcore/modules_gallvp/1' "./modules/gallvp/$1/tests/main.nf.test"
 }
 
-# Modules for tests
-cp -r ./nf-core-modules/modules/nf-core/gunzip ./modules/nf-core/
-
 # Modules for hybrid subworkflows
+cp_hybrid_module "gunzip"
 cp_hybrid_module "ltrfinder"
 cp_hybrid_module "ltrharvest"
 cp_hybrid_module "ltrretriever/ltrretriever"