release 1.1.2 - canguro

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 1.1.2 - canguro
+
+This release reverts the `wfmash` tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly.
+It is currently unclear, when a new _stable_ release will become available. People like @baozg or @AndreaGuarracino are evaluating.
+
+- Per default, we set the number of mappings in `wfmash` to `--n_haplotypes - 1`. Previously, this was set to `1`.
+- Deactivated parameter `wfmash_hg_filter_ani_diff`, because the older `wfmash` version does not support it.
+
 ## 1.1.1 - LATÜRNICH
 
 This release fixes some important bugs:

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pangenome/releases/tag/1.1.1" target="_blank">nf-core/pangenome</a>
+  This report has been generated by the <a href="https://github.com/nf-core/pangenome/releases/tag/1.1.2" target="_blank">nf-core/pangenome</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pangenome/1.1.1/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/pangenome/1.1.2/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pangenome-methods-description":
     order: -1000

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 = [

modules.json

@@ -82,7 +82,7 @@
                     },
                     "wfmash": {
                         "branch": "master",
-                        "git_sha": "0c49f318ec4701b891a87f25fb07b34713c90203",
+                        "git_sha": "77c0c76b7eb7ec564617e635953addc9fb40b61e",
                         "installed_by": ["modules"]
                     }
                 }

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
@@ -277,7 +277,7 @@ manifest {
     description     = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.1'
+    version         = '1.1.2'
     doi             = 'https://doi.org/10.5281/zenodo.8202636'
 }
 

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]."
                 }
             }
         },