Merge pull request #88 from nf-core/zn_release

chore: prepare for release
nf-core · Nov 6, 2024 · 6b1ec1e · 6b1ec1e
2 parents edf6172 + 5bc7de7
commit 6b1ec1e
Show file tree

Hide file tree

Showing 12 changed files with 36 additions and 27 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -23,5 +23,5 @@ template:
   org: nf-core
   outdir: .
   skip_features: null
-  version: 1.0.2dev
+  version: 1.0.2
 update: null
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,14 +3,21 @@
 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).
 
-## Unreleased
+## [[1.0.2]](https://github.com/nf-core/fastquorum/releases/tag/1.0.2) -- 2024-11-06
 
 ### Enhancements & fixes
 
 - [PR #87](https://github.com/nf-core/fastquorum/pull/87) - Raise minimum 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
 
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Simon Pearce](https://github.com/SPPearce)
+- [Zach Norgaard](https://github.com/znorgaard)
+
 ## [[1.0.1]](https://github.com/nf-core/fastquorum/releases/tag/1.0.1) -- 2024-09-10
 
 ### 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/tree/dev" target="_blank">nf-core/fastquorum</a>
+  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>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fastquorum/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fastquorum/1.0.2/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fastquorum-methods-description":
     order: -1000

diff --git a/modules.json b/modules.json
@@ -46,7 +46,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -56,7 +56,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

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         = '1.0.2dev'
+    version         = '1.0.2'
     doi             = '10.5281/zenodo.10456900,10.5281/zenodo.11267672'
 }
 

diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
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=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -26,7 +26,7 @@
     },
     "multi_fastq_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.8.4",

diff --git a/tests/pipeline/multi_lanes.nf.test.snap b/tests/pipeline/multi_lanes.nf.test.snap
@@ -1,13 +1,13 @@
 {
     "multi_lanes_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.2}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:44:11.374426"
+        "timestamp": "2024-10-31T14:39:27.884022"
     },
     "multi_lanes_ht": {
         "content": [
@@ -26,13 +26,13 @@
     },
     "multi_lanes_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.2}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, MERGE_BAM={samtools=1.21}, SORTBAM={fgbio=2.2.1}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-23T11:47:27.269353"
+        "timestamp": "2024-10-31T14:42:58.125095"
     },
     "multi_lanes_rd": {
         "content": [
@@ -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=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -21,7 +21,7 @@
     },
     "single_fastq_rd_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLMOLECULARCONSENSUSREADS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.8.4",

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=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLDDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, FILTERCONSENSUSREADS={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -11,7 +11,7 @@
     },
     "tiny_ht_software_versions": {
         "content": [
-            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2dev}}"
+            "{ALIGN_CONSENSUS_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, ALIGN_RAW_BAM={bwa=0.7.17-r1188, fgbio=2.0.2, samtools=1.16.1}, CALLANDFILTERDUPLEXCONSENSUSREADS={fgbio=2.0.2}, COLLECTDUPLEXSEQMETRICS={fgbio=2.0.2}, FASTQC={fastqc=0.12.1}, FASTQTOBAM={fgbio=2.0.2}, GROUPREADSBYUMI={fgbio=2.0.2}, Workflow={nf-core/fastquorum=v1.0.2}}"
         ],
         "meta": {
             "nf-test": "0.8.4",