diff --git a/.nf-core.yml b/.nf-core.yml index 5414532..ab64468 100644 --- 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 index 13944d7..b39a78a 100644 --- 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). -## Unreleased +## [[1.0.2]](https://github.com/nf-core/fastquorum/releases/tag/1.0.2) -- 2024-11-06 ### Enhancements & fixes @@ -11,6 +11,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [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 index c2b23db..d00fd2e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/fastquorum + This report has been generated by the nf-core/fastquorum analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-fastquorum-methods-description": order: -1000 diff --git a/modules.json b/modules.json index c243610..890a1bb 100644 --- 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 index dcb59f5..b02fe8d 100644 --- 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 index ca964ce..02dbf09 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc43..8fb3016 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 478fb8a..0907ac5 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -5,4 +5,4 @@ plugins { validation { parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" monochromeLogs = true -} +} \ No newline at end of file diff --git a/tests/pipeline/multi_fastq.nf.test.snap b/tests/pipeline/multi_fastq.nf.test.snap index 68b5e0b..982612c 100644 --- 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 index 2b3fda1..297a526 100644 --- 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" } -} +} \ No newline at end of file diff --git a/tests/pipeline/single_fastq.nf.test.snap b/tests/pipeline/single_fastq.nf.test.snap index d64b2ca..2d4eb90 100644 --- 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 index 8458ca3..d595bac 100644 --- 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",