Merge pull request #192 from nf-core/wfmash_0104

revert `wfmash` to v0.10.4
nf-core · Mar 25, 2024 · 5ece245 · 5ece245
2 parents 190fb05 + e9ee042
commit 5ece245
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Showing 11 changed files with 22 additions and 115 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -102,7 +102,7 @@ process {
     withName: WFMASH_MAP_ALIGN {
         ext.args = {
             [
-                "-n ${params.wfmash_n_mappings}",
+                params.wfmash_n_mappings       ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -113,8 +113,8 @@ process {
                 "-H ${params.wfmash_mash_kmer_thres}",
                 "${wfmash_sparse_map_cmd}",
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
-                "-2 ${params.wfmash_hg_filter_ani_diff}",
-                "--lower-triangular",
+//                "-2 ${params.wfmash_hg_filter_ani_diff}",
+//                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -127,7 +127,7 @@ process {
     withName: WFMASH_MAP {
         ext.args = {
             [
-                "-n ${params.wfmash_n_mappings}",
+                params.wfmash_n_mappings       ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -139,8 +139,8 @@ process {
                 "${wfmash_sparse_map_cmd}",
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-m",
-                "-2 ${params.wfmash_hg_filter_ani_diff}",
-                "--lower-triangular",
+//                "-2 ${params.wfmash_hg_filter_ani_diff}",
+//                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -153,7 +153,7 @@ process {
     withName: WFMASH_MAP_COMMUNITY {
         ext.args = {
             [
-                "-n ${params.wfmash_n_mappings}",
+                params.wfmash_n_mappings       ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -165,8 +165,8 @@ process {
                 "${wfmash_sparse_map_cmd}",
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-m",
-                "-2 ${params.wfmash_hg_filter_ani_diff}",
-                "--lower-triangular",
+//                "-2 ${params.wfmash_hg_filter_ani_diff}",
+//                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -188,7 +188,7 @@ process {
     withName: WFMASH_ALIGN {
         ext.args = {
             [
-                "-n ${params.wfmash_n_mappings}",
+                params.wfmash_n_mappings       ? "-n ${params.wfmash_n_mappings}": "-n ${params.n_haplotypes - 1}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -200,8 +200,8 @@ process {
                 "${wfmash_sparse_map_cmd}",
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "--invert-filtering",
-                "-2 ${params.wfmash_hg_filter_ani_diff}",
-                "--lower-triangular",
+//                "-2 ${params.wfmash_hg_filter_ani_diff}",
+//                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [

diff --git a/modules.json b/modules.json
@@ -82,7 +82,7 @@
                     },
                     "wfmash": {
                         "branch": "master",
-                        "git_sha": "0c49f318ec4701b891a87f25fb07b34713c90203",
+                        "git_sha": "77c0c76b7eb7ec564617e635953addc9fb40b61e",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml
diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf
diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml
diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test
diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap
diff --git a/modules/nf-core/wfmash/tests/nextflow.config b/modules/nf-core/wfmash/tests/nextflow.config
diff --git a/modules/nf-core/wfmash/tests/tags.yml b/modules/nf-core/wfmash/tests/tags.yml
diff --git a/nextflow.config b/nextflow.config
@@ -27,7 +27,7 @@ params {
     wfmash_only                 = false
     wfmash_temp_dir             = null
     wfmash_hg_filter_ani_diff   = 30
-    wfmash_n_mappings           = 1
+    wfmash_n_mappings           = null
 
     // Seqwish options
     seqwish_paf = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -122,8 +122,7 @@
                 },
                 "wfmash_n_mappings": {
                     "type": "integer",
-                    "default": 1,
-                    "description": "Number of mappings for each segment."
+                    "description": "Number of mappings for each segment. [default: n_haplotypes - 1]."
                 }
             }
         },