Merge pull request #99 from nf-core/zn_version_bump

chore: version bump
nf-core · Dec 2, 2024 · 34afc50 · 34afc50
2 parents d8443c1 + f751c7b
commit 34afc50
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Showing 8 changed files with 18 additions and 18 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -23,5 +23,5 @@ template:
   org: nf-core
   outdir: .
   skip_features: null
-  version: 1.0.2
+  version: 1.1.0
 update: null
diff --git a/CHANGELOG.md b/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).
 
-## [[1.0.2]](https://github.com/nf-core/fastquorum/releases/tag/1.0.2) -- 2024-12-02
+## [[1.1.0]](https://github.com/nf-core/fastquorum/releases/tag/1.1.0) -- 2024-12-02
 
 ### Enhancements & fixes
 
@@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PR #87](https://github.com/nf-core/fastquorum/pull/87) - Raise minimum Nextflow version to 24.04.2
 - [PR #84](https://github.com/nf-core/fastquorum/pull/84) - Update to nf-core/tools template version 3.0.2
-- [PR #79](https://github.com/nf-core/fastquorum/pull/79) and [PR #80](https://github.com/nf-core/fastquorum/pull/90) - Publish aligned consensus bai file
+- [PR #79](https://github.com/nf-core/fastquorum/pull/79) and [PR #80](https://github.com/nf-core/fastquorum/pull/80) - Publish aligned consensus bai file
 
 ### Credits
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fastquorum/releases/tag/1.0.2" target="_blank">nf-core/fastquorum</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fastquorum/releases/tag/1.1.0" target="_blank">nf-core/fastquorum</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fastquorum/1.0.2/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fastquorum/1.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fastquorum-methods-description":
     order: -1000

diff --git a/nextflow.config b/nextflow.config
@@ -241,7 +241,7 @@ manifest {
     description     = """fgbio Best Practices FASTQ to Consensus Pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0.2'
+    version         = '1.1.0'
     doi             = '10.5281/zenodo.10456900,10.5281/zenodo.11267672'
 }
 

diff --git a/tests/pipeline/multi_fastq.nf.test.snap b/tests/pipeline/multi_fastq.nf.test.snap
@@ -16,7 +16,7 @@
     },
     "multi_fastq_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -26,7 +26,7 @@
     },
     "multi_fastq_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -49,4 +49,4 @@
         },
         "timestamp": "2024-05-20T01:58:10.241449"
     }
-}
+}
diff --git a/tests/pipeline/multi_lanes.nf.test.snap b/tests/pipeline/multi_lanes.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "multi_lanes_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -26,7 +26,7 @@
     },
     "multi_lanes_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -49,4 +49,4 @@
         },
         "timestamp": "2024-05-20T01:34:44.993842"
     }
-}
+}
diff --git a/tests/pipeline/single_fastq.nf.test.snap b/tests/pipeline/single_fastq.nf.test.snap
@@ -11,7 +11,7 @@
     },
     "single_fastq_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -21,7 +21,7 @@
     },
     "single_fastq_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLMOLECULARCONSENSUSREADS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLMOLECULARCONSENSUSREADS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -39,4 +39,4 @@
         },
         "timestamp": "2024-11-13T16:32:31.496755"
     }
-}
+}
diff --git a/tests/pipeline/tiny.nf.test.snap b/tests/pipeline/tiny.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "tiny_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, FILTERCONSENSUSREADS={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -11,7 +11,7 @@
     },
     "tiny_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.0.2}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, ALIGN_RAW_BAM={bwa=0.7.18-r1243-dirty, fgbio=2.4.0, samtools=1.21}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.4.0}, COLLECTDUPLEXSEQMETRICS={fgbio=2.4.0}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.4.0}, GROUPREADSBYUMI={fgbio=2.4.0}, Workflow={nf-core/fastquorum=v1.1.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -41,4 +41,4 @@
         },
         "timestamp": "2024-05-19T23:48:57.112733"
     }
-}
+}