update swf msa_alignment to avoid dynamic includes

mirpedrol · Nov 6, 2024 · 34e891b · 34e891b
1 parent 4748294
commit 34e891b
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Showing 7 changed files with 238 additions and 416 deletions.
diff --git a/modules/mirpedrol/kalign/align/tests/main.nf.test b/modules/mirpedrol/kalign/align/tests/main.nf.test
@@ -26,7 +26,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta")},
+                { assert snapshot(process.out.alignment).match("alignment")},
+                { assert snapshot(process.out.versions).match("versions")}
             )
         }
     }

diff --git a/modules/mirpedrol/mafft/tests/main.nf.test b/modules/mirpedrol/mafft/tests/main.nf.test
@@ -23,7 +23,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta")}
+                { assert snapshot(process.out.alignment).match("alignment")},
+                { assert snapshot(process.out.versions).match("mafft_versions")}
             )
         }
 

diff --git a/modules/mirpedrol/muscle5/super5/meta.yml b/modules/mirpedrol/muscle5/super5/meta.yml
@@ -7,7 +7,7 @@ keywords:
   - msa
   - multiple sequence alignment
   - msa
-  - align
+  - alignment
 tools:
   - muscle-super5:
       description: "Muscle v5 is a major re-write of MUSCLE based on new algorithms."
@@ -29,7 +29,7 @@ input:
     - fasta:
         type: file
         description: Input sequences for alignment must be in FASTA format
-        pattern: "*.{fasta,fa,fna}"
+        pattern: "*.{fa,fasta}"
         ontologies:
           - edam: http://edamontology.org/format_1929
 output:

diff --git a/subworkflows/mirpedrol/msa_alignment/main.nf b/subworkflows/mirpedrol/msa_alignment/main.nf
@@ -1,57 +1,66 @@
+include { MAFFT } from '../../../modules/mirpedrol/mafft/main'
+include { KALIGN_ALIGN } from '../../../modules/mirpedrol/kalign/align/main'
+include { FAMSA_ALIGN } from '../../../modules/mirpedrol/famsa/align/main'
+include { MUSCLE5_SUPER5 } from '../../../modules/mirpedrol/muscle5/super5/main'
+include { MAGUS_ALIGN } from '../../../modules/mirpedrol/magus/align/main'
 include { CLUSTALO_ALIGN } from '../../../modules/mirpedrol/clustalo/align/main'
-include { FAMSA_ALIGN    } from '../../../modules/mirpedrol/famsa/align/main'
-include { KALIGN_ALIGN   } from '../../../modules/mirpedrol/kalign/align/main'
+include { TCOFFEE_ALIGN } from '../../../modules/mirpedrol/tcoffee/align/main'
 include { LEARNMSA_ALIGN } from '../../../modules/mirpedrol/learnmsa/align/main'
-include { MAFFT          } from '../../../modules/mirpedrol/mafft/main'
-include { MAGUS_ALIGN    } from '../../../modules/mirpedrol/magus/align/main'
-include { MUSCLE5_SUPER5 } from '../../../modules/mirpedrol/muscle5/super5/main'
-include { TCOFFEE_ALIGN  } from '../../../modules/mirpedrol/tcoffee/align/main'
+
 
 workflow MSA_ALIGNMENT {
 
     take:
-    ch_fasta // channel: [ meta, fasta ]
+    ch_fasta
 
     main:
-    def ch_out_alignment = Channel.empty()
-    def ch_versions = Channel.empty()
-
-    if ( params.aligner == "clustalo/align" ) {
-        CLUSTALO_ALIGN( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(CLUSTALO_ALIGN.out.alignment)
-        ch_versions = ch_versions.mix(CLUSTALO_ALIGN.out.versions.first())
-    } else if ( params.aligner == "famsa/align" ) {
-        FAMSA_ALIGN( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(FAMSA_ALIGN.out.alignment)
-        ch_versions = ch_versions.mix(FAMSA_ALIGN.out.versions.first())
-    } else if ( params.aligner == "kalign/align" ) {
-        KALIGN_ALIGN( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(KALIGN_ALIGN.out.alignment)
-        ch_versions = ch_versions.mix(KALIGN_ALIGN.out.versions.first())
-    } else if ( params.aligner == "learnmsa/align" ) {
-        LEARNMSA_ALIGN( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment)
-        ch_versions = ch_versions.mix(LEARNMSA_ALIGN.out.versions.first())
-    } else if ( params.aligner == "mafft" ) {
-        MAFFT( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(MAFFT.out.alignment)
-        ch_versions = ch_versions.mix(MAFFT.out.versions.first())
-    } else if ( params.aligner == "magus/align" ) {
-        MAGUS_ALIGN( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(MAGUS_ALIGN.out.alignment)
-        ch_versions = ch_versions.mix(MAGUS_ALIGN.out.versions.first())
-    } else if ( params.aligner == "muscle5/super5" ) {
-        MUSCLE5_SUPER5( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(MUSCLE5_SUPER5.out.alignment)
-        ch_versions = ch_versions.mix(MUSCLE5_SUPER5.out.versions.first())
-    } else if ( params.aligner == "tcoffee/align" ) {
-        TCOFFEE_ALIGN( ch_fasta )
-        ch_out_alignment = ch_out_alignment.mix(TCOFFEE_ALIGN.out.alignment)
-        ch_versions = ch_versions.mix(TCOFFEE_ALIGN.out.versions.first())
-    }
+	def ch_out_alignment = Channel.empty()
+	def ch_out_versions = Channel.empty()
+	if ( params.alignment == "mafft" ) {
+		MAFFT( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(MAFFT.out.alignment)
+		ch_out_versions = ch_out_versions.mix(MAFFT.out.versions)
+	}
+	else if ( params.alignment == "kalign/align" ) {
+		KALIGN_ALIGN( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(KALIGN_ALIGN.out.alignment)
+		ch_out_versions = ch_out_versions.mix(KALIGN_ALIGN.out.versions)
+	}
+	else if ( params.alignment == "famsa/align" ) {
+		FAMSA_ALIGN( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(FAMSA_ALIGN.out.alignment)
+		ch_out_versions = ch_out_versions.mix(FAMSA_ALIGN.out.versions)
+	}
+	else if ( params.alignment == "muscle5/super5" ) {
+		MUSCLE5_SUPER5( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(MUSCLE5_SUPER5.out.alignment)
+		ch_out_versions = ch_out_versions.mix(MUSCLE5_SUPER5.out.versions)
+	}
+	else if ( params.alignment == "magus/align" ) {
+		MAGUS_ALIGN( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(MAGUS_ALIGN.out.alignment)
+		ch_out_versions = ch_out_versions.mix(MAGUS_ALIGN.out.versions)
+	}
+	else if ( params.alignment == "clustalo/align" ) {
+		CLUSTALO_ALIGN( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(CLUSTALO_ALIGN.out.alignment)
+		ch_out_versions = ch_out_versions.mix(CLUSTALO_ALIGN.out.versions)
+	}
+	else if ( params.alignment == "tcoffee/align" ) {
+		TCOFFEE_ALIGN( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(TCOFFEE_ALIGN.out.alignment)
+		ch_out_versions = ch_out_versions.mix(TCOFFEE_ALIGN.out.versions)
+	}
+	else if ( params.alignment == "learnmsa/align" ) {
+		LEARNMSA_ALIGN( ch_fasta )
+		ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment)
+		ch_out_versions = ch_out_versions.mix(LEARNMSA_ALIGN.out.versions)
+	}
+
 
     emit:
-    alignment = ch_out_alignment // channel: [ meta, *.aln.gz ]
-    versions  = ch_versions      // channel: [ versions.yml ]
+	alignment = ch_out_alignment
+	versions = ch_out_versions
+
 }
 
diff --git a/subworkflows/mirpedrol/msa_alignment/meta.yml b/subworkflows/mirpedrol/msa_alignment/meta.yml
@@ -1,38 +1,62 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/mirpedrol/class-modules/main/subworkflows/yaml-schema.json
 name: "msa_alignment"
-description: Perform a multiple sequence alignment with one of the possible aligners
-keywords:
-  - alignment
-  - MSA
-  - genomics
+description: Perform multiple sequence alignment
+keywords: ["alignment", "msa", "align"]
 components:
-  - clustalo/align
-  - famsa/align
-  - kalign/align
-  - learnmsa/align
-  - mafft
-  - magus/align
-  - muscle5/super5
-  - tcoffee/align
+  [
+    "mafft",
+    "kalign/align",
+    "famsa/align",
+    "muscle5/super5",
+    "magus/align",
+    "clustalo/align",
+    "tcoffee/align",
+    "learnmsa/align",
+  ]
+
 input:
   - ch_fasta:
-      type: file
-      description: |
-        Structure: [ val(meta), path(fasta) ]
-        meta: Groovy Map containing sample information
-        fasta: Input sequences in FASTA format (*.{fa,fasta})
+      description: "Channel containing: meta, fasta"
+      structure:
+        - meta:
+            description: "Groovy Map containing sample information
+
+              e.g. `[ id:'sample1', single_end:false ]`
+
+              "
+            type: map
+        - fasta:
+            description: Input sequences in FASTA format
+            ontologies:
+              - edam: http://edamontology.org/format_1929
+            pattern: "*.{fa,fasta}"
+            type: file
+
 output:
   - alignment:
-      type: file
-      description: |
-        Structure: [ val(meta), path(alignment) ]
-        meta: Groovy Map containing sample information
-        alignment: Alignment file, in gzipped fasta format (*.aln.gz)
+      description: Output channel alignment
+      structure:
+        - meta:
+            description: "Groovy Map containing sample information
+
+              e.g. `[ id:'test']`
+
+              "
+            type: map
+        - "*.aln.gz":
+            description: Alignment file, in FASTA format.
+            ontologies:
+              - edam: http://edamontology.org/format_1984
+            pattern: "*.aln.gz"
+            type: file
   - versions:
-      type: file
-      description: |
-        File containing software versions
-        Structure: [ path(versions.yml) ]
+      description: Output channel versions
+      structure:
+        - versions.yml:
+            description: File containing software versions
+            pattern: versions.yml
+            type: file
+
 authors:
   - "@mirpedrol"
 maintainers: