refactor: Use fastx/collapser from nf-core (#34)

Signed-off-by: jvfe <[email protected]>
dalmolingroup · Mar 31, 2024 · b263237 · b263237
1 parent 8efe0a2
commit b263237
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Showing 10 changed files with 261 additions and 35 deletions.
diff --git a/modules.json b/modules.json
@@ -59,6 +59,14 @@
                             "modules"
                         ]
                     },
+                    "fastx/collapser": {
+                        "branch": "master",
+                        "git_sha": "210e7c8f33f8ca0e35e027aa8889d03205a57b88",
+                        "installed_by": [
+                            "modules"
+                        ],
+                        "patch": "modules/nf-core/fastx/collapser/fastx-collapser.diff"
+                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",

diff --git a/modules/local/fastx_toolkit/collapser.nf b/modules/local/fastx_toolkit/collapser.nf
diff --git a/modules/nf-core/fastx/collapser/environment.yml b/modules/nf-core/fastx/collapser/environment.yml
diff --git a/modules/nf-core/fastx/collapser/fastx-collapser.diff b/modules/nf-core/fastx/collapser/fastx-collapser.diff
diff --git a/modules/nf-core/fastx/collapser/main.nf b/modules/nf-core/fastx/collapser/main.nf
diff --git a/modules/nf-core/fastx/collapser/meta.yml b/modules/nf-core/fastx/collapser/meta.yml
diff --git a/modules/nf-core/fastx/collapser/tests/main.nf.test b/modules/nf-core/fastx/collapser/tests/main.nf.test
diff --git a/modules/nf-core/fastx/collapser/tests/main.nf.test.snap b/modules/nf-core/fastx/collapser/tests/main.nf.test.snap
diff --git a/modules/nf-core/fastx/collapser/tests/tags.yml b/modules/nf-core/fastx/collapser/tests/tags.yml
diff --git a/workflows/euryale.nf b/workflows/euryale.nf
@@ -36,7 +36,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
 //
 // MODULES
 //
-include { FASTX_COLLAPSER } from '../modules/local/fastx_toolkit/collapser'
 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
@@ -59,6 +58,7 @@ include { FUNCTIONAL } from '../subworkflows/local/functional'
 // MODULE: Installed directly from nf-core/modules
 //
 include { GUNZIP } from '../modules/nf-core/gunzip/main'
+include { FASTX_COLLAPSER } from '../modules/nf-core/fastx/collapser'
 include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
@@ -143,7 +143,7 @@ workflow EURYALE {
             decompressed_reads
         )
 
-        FASTX_COLLAPSER.out.collapsed.set { clean_reads }
+        FASTX_COLLAPSER.out.fasta.set { clean_reads }
     }
 
      if (!params.skip_alignment) {