pre-release dev

.nf-core.yml

@@ -9,7 +9,7 @@ template:
   name: bactmap
   description: A mapping-based pipeline for bacterial whole genome sequences
   author: Andries J. van Tonder
-  version: 2.0.0dev
+  version: 2.0.0
   force: true
   outdir: .
   skip_features: []

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v2.0.0dev - [date]
+## 2.0.0 - Titanium Bird - 2025-09-15
 
 nf-core/bactmap release v2.0.0. The pipeline has been completely rewritten using a fresh template created with [nf-core](https://nf-co.re/).
 

assets/multiqc_config.yml

@@ -1,9 +1,10 @@
 # multiqc_config.yml
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/bactmap/tree/dev" target="_blank">nf-core/bactmap</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/bactmap/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/bactmap/releases/tag/2.0.0"
+  target="_blank">nf-core/bactmap</a> analysis pipeline. For information about how
+  to interpret these results, please see the <a href="https://nf-co.re/bactmap/2.0.0/docs/output"
+  target="_blank">documentation</a>.
 
 # Report section order
 report_section_order:
@@ -106,7 +107,8 @@ top_modules:
       anchor: "filtlong"
       target: "Filtlong"
       doi: "10.1371/journal.pcbi.1010905"
-      info: "This section of the report shows Filtlong results for reads after length filtering."
+      info: "This section of the report shows Filtlong results for reads after length
+        filtering."
       path_filters:
         - "*filtlong/*"
       extra: |
@@ -129,15 +131,17 @@ top_modules:
       anchor: "samtools"
       target: "SAMTools"
       doi: "10.1093/bioinformatics/btp352"
-      info: "This section of the report shows SAMTools counts/statistics after mapping with Bowtie 2/BWA 2 mem."
+      info: "This section of the report shows SAMTools counts/statistics after mapping
+        with Bowtie 2/BWA 2 mem."
       path_filters:
         - "*.stats"
   - "bcftools":
       name: "BCFTools"
       anchor: "bcftools"
       target: "BCFTools"
       doi: "10.1093/bioinformatics/btp352"
-      info: "This section of the report shows BCFTools stats results for the called variants."
+      info: "This section of the report shows BCFTools stats results for the called
+        variants."
       path_filters:
         - "*.txt"
 

modules.json

@@ -12,27 +12,27 @@
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
                         "installed_by": ["modules"]
                     },
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
                         "installed_by": ["bam_variant_calling_sort_freebayes_bcftools"]
                     },
                     "bcftools/query": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
                         "installed_by": ["modules"]
                     },
                     "bcftools/sort": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
                         "installed_by": ["bam_variant_calling_sort_freebayes_bcftools"]
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
                         "installed_by": ["modules"]
                     },
                     "bedtools/subtract": {
@@ -72,7 +72,7 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
@@ -132,32 +132,32 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "e89ff68a46b848c4d8aabb8569767516d46db319",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "seqtk/comp": {
@@ -176,7 +176,7 @@
                 "nf-core": {
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {