adding align and consensus contigs (not tested)

Joon-Klaps · Jul 6, 2023 · f98b495 · f98b495
1 parent 058dfd6
commit f98b495
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Showing 10 changed files with 376 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -274,7 +274,6 @@ process {
                 ]
             }
 
-
             withName: ".*:FASTA_BLAST_CLUST:CAT_CAT" {
             ext.prefix = { "${meta.id}.fa.gz" }
             publishDir = [
@@ -366,6 +365,33 @@ process {
                     pattern: "*.fa.gz"
                 ]
             }
+
+            withName: MUSCLE {
+                ext.args = "-fasta -maketree"
+                publishDir = [
+                    path: { "${params.outdir}/polishing/intermediate/alignment/muscle" },
+                    mode: params.publish_dir_mode,
+                    enabled: params.save_intermediate_polishing,
+                    pattern: "*.{afa,tree)"
+                ]
+            }
+
+            withName: MAFFT {
+                ext.args = "--adjustdirection --maxiterate 100"
+                publishDir = [
+                    path: { "${params.outdir}/polishing/intermediate/alignment/mafft" },
+                    mode: params.publish_dir_mode,
+                    enabled: params.save_intermediate_polishing,
+                    pattern: "*.{fas)"
+                ]
+            }
+
+            withName: ".*:ALIGN_COLLAPSE_CONTIGS:CAT_CAT" {
+            ext.prefix = { "${meta.id}.fa" }
+            publishDir = [
+                enabled: false
+                ]
+            }
         }
     }
 

diff --git a/modules.json b/modules.json
@@ -42,10 +42,14 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "emboss/cons": {
+                        "branch": "master",
+                        "git_sha": "0739c1b680ea60f5a83e7f5071008627ddc436ce",
+                        "installed_by": ["modules"]
+                    },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
@@ -76,6 +80,11 @@
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
                         "installed_by": ["modules"]
                     },
+                    "mafft": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
                     "megahit": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
@@ -96,6 +105,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "muscle": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/nf-core/emboss/cons/main.nf b/modules/nf-core/emboss/cons/main.nf
diff --git a/modules/nf-core/emboss/cons/meta.yml b/modules/nf-core/emboss/cons/meta.yml
diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf
diff --git a/modules/nf-core/mafft/meta.yml b/modules/nf-core/mafft/meta.yml
diff --git a/modules/nf-core/muscle/main.nf b/modules/nf-core/muscle/main.nf
diff --git a/modules/nf-core/muscle/meta.yml b/modules/nf-core/muscle/meta.yml