Some fixes (docs/combgc)

CHANGELOG.md

@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#391](https://github.com/nf-core/funcscan/pull/391) Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated docs. (by @jasmezz)
 - [#391](https://github.com/nf-core/funcscan/pull/391) Made all "database" parameter names consistent. (by @jasmezz)
 - [#397](https://github.com/nf-core/funcscan/pull/397) Removed deprecated AMPcombi module, fixed variable name in BGC workflow, updated minor parts in docs (usage, parameter schema). (by @jasmezz)
+- [#402](https://github.com/nf-core/funcscan/pull/402) Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)
 
 ### `Dependencies`
 
@@ -43,13 +44,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | AMRFinderPlus | 3.11.18          | 3.12.8      |
 | antiSMASH     | 6.1.1            | 7.1.0       |
 | bioawk        | 1.0              | NA          |
+| comBGC        | 1.6.1            | 1.6.2       |
 | DeepARG       | 1.0.2            | 1.0.4       |
 | DeepBGC       | 0.1.30           | 0.1.31      |
 | GECCO         | 0.9.8            | 0.9.10      |
 | hAMRonization | 1.1.1            | 1.1.4       |
 | HMMER         | 3.3.2            | 3.4         |
 | MMSeqs        | NA               | 2:15.6f452  |
-| MultiQC       | 1.15             | 1.22.3      |
+| MultiQC       | 1.15             | 1.23        |
 | Pyrodigal     | 2.1.0            | 3.3.0       |
 | RGI           | 5.2.1            | 6.0.3       |
 | seqkit        | NA               | 2.8.1       |
@@ -58,7 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Deprecated`
 
 - [#384](https://github.com/nf-core/funcscan/pull/384) Deprecated AMPcombi and exchanged it with full suite of AMPcombi2 submodules. (by @darcy220606)
-- [#382](https://github.com/nf-core/funcscan/pull/382) Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. Bioawk is replaced with seqkit (by @jfy133, @darcy220606)
+- [#382](https://github.com/nf-core/funcscan/pull/382) Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. Bioawk is replaced with seqkit. (by @jfy133, @darcy220606)
 
 ## v1.1.6 - [2024-07-08]
 
@@ -94,7 +96,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#306](https://github.com/nf-core/funcscan/pull/306) Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
-- [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
+- [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database. (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
 - [#310](https://github.com/nf-core/funcscan/pull/310) Fixed error when supplying uncompressed input; added "fas" file extension for FASTA files. (by @tavareshugo)
 - [#311](https://github.com/nf-core/funcscan/pull/311) Merged pipeline template of nf-core/tools version 2.10. (by @jasmezz)
 

bin/comBGC.py

@@ -35,7 +35,7 @@
 SOFTWARE.
 """
 
-tool_version = "0.6.1"
+tool_version = "0.6.2"
 welcome = """\
                 ........................
                     * comBGC v.{version} *
@@ -307,7 +307,7 @@ def antismash_workflow(antismash_paths):
                         feature.location.start + 1
                     )  # +1 because zero-based start position
                     BGC_end = feature.location.end
-                    BGC_length = feature.location.end - feature.location.start + 1
+                    BGC_length = feature.location.end - feature.location.start
 
                     # If there are knownclusterblast files for the BGC, get MIBiG IDs of their homologs
                     if kcb_files:

docs/output.md

@@ -46,7 +46,7 @@ results/
 |   └── seqkit/
 ├── reports/
 |   ├── ampcombi/
-|   ├── comBGC/
+|   ├── combgc/
 |   └── hamronization_summarize/
 ├── databases/
 ├── multiqc/

modules.json

@@ -47,12 +47,12 @@
                     },
                     "antismash/antismashlite": {
                         "branch": "master",
-                        "git_sha": "39c00d0873ff072b2901d8ae1f36abe1522c90f2",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "antismash/antismashlitedownloaddatabases": {
                         "branch": "master",
-                        "git_sha": "6c7bac5e7c4c00c43803df47e7db5d0c344b7ac4",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "bakta/bakta": {
@@ -97,7 +97,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "hamronization/abricate": {
@@ -147,7 +147,7 @@
                     },
                     "mmseqs/createtsv": {
                         "branch": "master",
-                        "git_sha": "5d849d54f06174c3313eb50c776d4916912db16b",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "mmseqs/databases": {
@@ -162,7 +162,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "314d742bdb357a1df5f9b88427b3b6ac78aa33f7",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
@@ -187,7 +187,7 @@
                     },
                     "rgi/main": {
                         "branch": "master",
-                        "git_sha": "0ae1adbee6a09b4c5097e990b2db1f5ebe96265c",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "seqkit/seq": {
@@ -202,8 +202,9 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["modules"]
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/untar/untar.diff"
                     }
                 }
             },