diff --git a/CHANGELOG.md b/CHANGELOG.md
index 723d4a83..ca109cb2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,18 @@
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).
+## nf-core/ampliseq version 2.9.0dev
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Removed`
+
## nf-core/ampliseq version 2.8.0 - 2024-01-16
### `Added`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index af96c9d1..eaf9f190 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/ampliseq
+ This report has been generated by the nf-core/ampliseq
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-ampliseq-methods-description":
order: -1000
diff --git a/nextflow.config b/nextflow.config
index 903eda54..8e356611 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -338,7 +338,7 @@ manifest {
description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '2.8.0'
+ version = '2.9.0dev'
doi = '10.5281/zenodo.1493841'
}
diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap
index 7cb5f68a..fba0c40b 100644
--- a/tests/pipeline/doubleprimers.nf.test.snap
+++ b/tests/pipeline/doubleprimers.nf.test.snap
@@ -13,7 +13,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, KRAKEN2_KRAKEN2={kraken2=2.1.2, pigz=2.6}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, KRAKEN2_KRAKEN2={kraken2=2.1.2, pigz=2.6}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-07-27T13:49:03+0000"
},
diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap
index c049085c..70bcf042 100644
--- a/tests/pipeline/fasta.nf.test.snap
+++ b/tests/pipeline/fasta.nf.test.snap
@@ -7,7 +7,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FILTER_CODONS={pandas=1.1.5, python=3.9.1}, FILTER_LEN_ASV={Biostrings=2.58.0, R=4.0.3}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FILTER_CODONS={pandas=1.1.5, python=3.9.1}, FILTER_LEN_ASV={Biostrings=2.58.0, R=4.0.3}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-05-28T21:06:17+0000"
},
diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap
index 989cbd59..20342347 100644
--- a/tests/pipeline/iontorrent.nf.test.snap
+++ b/tests/pipeline/iontorrent.nf.test.snap
@@ -13,7 +13,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-06-20T01:42:35+0000"
},
diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap
index 913b3818..c5492d96 100644
--- a/tests/pipeline/multi.nf.test.snap
+++ b/tests/pipeline/multi.nf.test.snap
@@ -14,7 +14,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-05-28T21:15:03+0000"
},
diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap
index e6c17e7f..0591a632 100644
--- a/tests/pipeline/novaseq.nf.test.snap
+++ b/tests/pipeline/novaseq.nf.test.snap
@@ -7,7 +7,7 @@
},
"software_versions": {
"content": [
- "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_CODONS={pandas=1.1.5, python=3.9.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_CODONS={pandas=1.1.5, python=3.9.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-06-20T00:10:02+0000"
},
diff --git a/tests/pipeline/pacbio_its.nf.test.snap b/tests/pipeline/pacbio_its.nf.test.snap
index 3cbdef01..43c873cf 100644
--- a/tests/pipeline/pacbio_its.nf.test.snap
+++ b/tests/pipeline/pacbio_its.nf.test.snap
@@ -35,7 +35,7 @@
},
"software_versions": {
"content": [
- "{ASSIGNSH={pandas=1.1.5, python=3.9.1}, BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FORMAT_TAXRESULTS_STD={pandas=1.1.5, python=3.9.1}, ITSX_CUTASV={ITSx=1.1.3}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_USEARCHGLOBAL={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{ASSIGNSH={pandas=1.1.5, python=3.9.1}, BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FORMAT_TAXRESULTS_STD={pandas=1.1.5, python=3.9.1}, ITSX_CUTASV={ITSx=1.1.3}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_USEARCHGLOBAL={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-06-20T02:07:02+0000"
},
diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap
index c8c3a9f1..6e7e9ca6 100644
--- a/tests/pipeline/pplace.nf.test.snap
+++ b/tests/pipeline/pplace.nf.test.snap
@@ -8,7 +8,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, EPANG_PLACE={epang=0.3.8}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, GAPPA_ASSIGN={gappa=0.8.0}, GAPPA_GRAFT={gappa=0.8.0}, GAPPA_HEATTREE={gappa=0.8.0}, HMMER_AFAFORMATQUERY={hmmer/easel=0.48}, HMMER_AFAFORMATREF={hmmer/easel=0.48}, HMMER_HMMALIGNQUERY={hmmer=3.3.2}, HMMER_HMMALIGNREF={hmmer=3.3.2}, HMMER_HMMBUILD={hmmer=3.3.2}, HMMER_MASKQUERY={hmmer/easel=0.48}, HMMER_MASKREF={hmmer/easel=0.48}, HMMER_UNALIGNREF={hmmer/easel=0.48}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, EPANG_PLACE={epang=0.3.8}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, GAPPA_ASSIGN={gappa=0.8.0}, GAPPA_GRAFT={gappa=0.8.0}, GAPPA_HEATTREE={gappa=0.8.0}, HMMER_AFAFORMATQUERY={hmmer/easel=0.48}, HMMER_AFAFORMATREF={hmmer/easel=0.48}, HMMER_HMMALIGNQUERY={hmmer=3.3.2}, HMMER_HMMALIGNREF={hmmer=3.3.2}, HMMER_HMMBUILD={hmmer=3.3.2}, HMMER_MASKQUERY={hmmer/easel=0.48}, HMMER_MASKREF={hmmer/easel=0.48}, HMMER_UNALIGNREF={hmmer/easel=0.48}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-06-20T17:24:03+0000"
},
diff --git a/tests/pipeline/qiimecustom.nf.test.snap b/tests/pipeline/qiimecustom.nf.test.snap
index 5f758fd4..5a9d3126 100644
--- a/tests/pipeline/qiimecustom.nf.test.snap
+++ b/tests/pipeline/qiimecustom.nf.test.snap
@@ -13,7 +13,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-05-28T21:18:54+0000"
},
diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap
index 4bfd8c2d..22db2252 100644
--- a/tests/pipeline/reftaxcustom.nf.test.snap
+++ b/tests/pipeline/reftaxcustom.nf.test.snap
@@ -13,7 +13,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, KRAKEN2_KRAKEN2={kraken2=2.1.2, pigz=2.6}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, KRAKEN2_KRAKEN2={kraken2=2.1.2, pigz=2.6}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-05-28T21:18:54+0000"
},
diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap
index 1b6e33c0..44977b82 100644
--- a/tests/pipeline/single.nf.test.snap
+++ b/tests/pipeline/single.nf.test.snap
@@ -13,7 +13,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-05-28T20:35:33+0000"
},
diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap
index fed045a4..03e44107 100644
--- a/tests/pipeline/sintax.nf.test.snap
+++ b/tests/pipeline/sintax.nf.test.snap
@@ -16,7 +16,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, ITSX_CUTASV={ITSx=1.1.3}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, ITSX_CUTASV={ITSx=1.1.3}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-06-20T16:40:18+0000"
},
diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap
index 8441f2a5..89702ac1 100644
--- a/tests/pipeline/test.nf.test.snap
+++ b/tests/pipeline/test.nf.test.snap
@@ -22,7 +22,7 @@
},
"software_versions": {
"content": [
- "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_CLUSTERS={pandas=1.1.5, python=3.9.1}, FILTER_LEN_ASV={Biostrings=2.58.0, R=4.0.3}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, VSEARCH_CLUSTER={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.8.0}}"
+ "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.3.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.3.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.3.1, ShortRead=1.58.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.3.1, dada2=1.28.0}, FASTQC={fastqc=0.12.1}, FILTER_CLUSTERS={pandas=1.1.5, python=3.9.1}, FILTER_LEN_ASV={Biostrings=2.58.0, R=4.0.3}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, VSEARCH_CLUSTER={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.9.0dev}}"
],
"timestamp": "2023-05-28T20:55:32+0000"
},