Merge pull request #2 from charles-plessy/addseqtk

Add seqtk modules
nf-core · Jun 19, 2024 · 62518a2 · 62518a2
2 parents 5b3fa86 + 57fd146
commit 62518a2
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diff --git a/modules.json b/modules.json
@@ -49,6 +49,11 @@
                         "branch": "master",
                         "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0",
                         "installed_by": ["modules"]
+                    },
+                    "seqtk/cutn": {
+                        "branch": "master",
+                        "git_sha": "7f88aae93c69586c0789322b77743ee0ef469502",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/nf-core/seqtk/cutn/environment.yml b/modules/nf-core/seqtk/cutn/environment.yml
diff --git a/modules/nf-core/seqtk/cutn/main.nf b/modules/nf-core/seqtk/cutn/main.nf
diff --git a/modules/nf-core/seqtk/cutn/meta.yml b/modules/nf-core/seqtk/cutn/meta.yml
diff --git a/modules/nf-core/seqtk/cutn/tests/main.nf.test b/modules/nf-core/seqtk/cutn/tests/main.nf.test
diff --git a/modules/nf-core/seqtk/cutn/tests/main.nf.test.snap b/modules/nf-core/seqtk/cutn/tests/main.nf.test.snap
diff --git a/modules/nf-core/seqtk/cutn/tests/tags.yml b/modules/nf-core/seqtk/cutn/tests/tags.yml
diff --git a/workflows/pairgenomealign.nf b/workflows/pairgenomealign.nf
@@ -6,6 +6,8 @@
 
 include { ASSEMBLYSCAN           } from '../modules/nf-core/assemblyscan/main'
 include { PAIRALIGN_M2M          } from '../subworkflows/local/pairalign_m2m/main'
+include { SEQTK_CUTN as SEQTK_CUTN_TARGET  } from '../modules/nf-core/seqtk/cutn/main'
+include { SEQTK_CUTN as SEQTK_CUTN_QUERY  } from '../modules/nf-core/seqtk/cutn/main'
 include { PAIRALIGN_M2O          } from '../subworkflows/local/pairalign_m2o/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
@@ -30,6 +32,20 @@ workflow PAIRGENOMEALIGN {
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
+    //
+    // MODULE: seqtk_cutn_target
+    //
+    SEQTK_CUTN_TARGET (
+        ch_targetgenome
+    )
+
+    //
+    // MODULE: seqtk_cutn_query
+    //
+    SEQTK_CUTN_QUERY (
+        ch_samplesheet
+    )
+
     //
     // MODULE: assembly-scan
     //