From 16a826559cb902285ce3ae8a00b3a5cb247434af Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 19 Oct 2023 16:41:12 +0200 Subject: [PATCH 01/17] bump version to 2.8.0dev --- CHANGELOG.md | 12 ++++++++++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- tests/pipeline/doubleprimers.nf.test.snap | 2 +- tests/pipeline/fasta.nf.test.snap | 2 +- tests/pipeline/iontorrent.nf.test.snap | 2 +- tests/pipeline/multi.nf.test.snap | 2 +- tests/pipeline/novaseq.nf.test.snap | 2 +- tests/pipeline/pacbio_its.nf.test.snap | 2 +- tests/pipeline/pplace.nf.test.snap | 2 +- tests/pipeline/reftaxcustom.nf.test.snap | 2 +- tests/pipeline/single.nf.test.snap | 2 +- tests/pipeline/sintax.nf.test.snap | 2 +- tests/pipeline/test.nf.test.snap | 2 +- 14 files changed, 26 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d4313bc..ddb0e72c 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 2.8.0dev + +### `Added` + +### `Changed` + +### `Fixed` + +### `Dependencies` + +### `Removed` + ## nf-core/ampliseq version 2.7.0 - 2023-10-20 ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8613d28d..64df13db 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 7b90f100..5139e0ec 100644 --- a/nextflow.config +++ b/nextflow.config @@ -329,7 +329,7 @@ manifest { description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.7.0' + version = '2.8.0dev' doi = '10.5281/zenodo.1493841' } diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap index 7c59fc97..d7cc9dce 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=3.11.4, yaml=6.0}, 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}, 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=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, 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=2.8.0dev}}" ], "timestamp": "2023-07-27T13:49:03+0000" }, diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap index b8894c92..6350712f 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "timestamp": "2023-05-28T21:06:17+0000" }, diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap index 6d36ce3b..420b3dd6 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "timestamp": "2023-06-20T01:42:35+0000" }, diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index 98fae3c6..2c0382f0 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=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.8.0dev}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap index 8b56978a..427cd40b 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "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 f26be552..c211e2b6 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{ASSIGNSH={pandas=1.1.5, python=3.9.1}, BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "timestamp": "2023-06-20T02:07:02+0000" }, diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index e16b3e86..4f64efa8 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap index 7ca4c208..7dca4e3e 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=3.11.4, yaml=6.0}, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0dev}}" ], "timestamp": "2023-05-28T21:18:54+0000" }, diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap index 77572d5d..a31b986c 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "timestamp": "2023-05-28T20:35:33+0000" }, diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index 1c19892e..069c7fa8 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=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.8.0dev}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index d3b9e8ac..967f1369 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=3.11.4, yaml=6.0}, 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=2.7.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.8.0dev}}" ], "timestamp": "2023-05-28T20:55:32+0000" }, From 4d334b97068d51ec1e1a7040579d3901ea7cf5c9 Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 3 Nov 2023 09:15:57 +0100 Subject: [PATCH 02/17] export MPLCONFIGDIR --- modules/local/qiime2_alphararefaction.nf | 1 + modules/local/qiime2_ancom_asv.nf | 1 + modules/local/qiime2_ancom_tax.nf | 1 + modules/local/qiime2_barplot.nf | 1 + modules/local/qiime2_classify.nf | 1 + modules/local/qiime2_diversity_adonis.nf | 1 + modules/local/qiime2_diversity_alpha.nf | 1 + modules/local/qiime2_diversity_beta.nf | 1 + modules/local/qiime2_diversity_betaord.nf | 1 + modules/local/qiime2_diversity_core.nf | 1 + modules/local/qiime2_export_absolute.nf | 1 + modules/local/qiime2_export_relasv.nf | 1 + modules/local/qiime2_export_reltax.nf | 1 + modules/local/qiime2_extract.nf | 1 + modules/local/qiime2_featuretable_group.nf | 1 + modules/local/qiime2_filtersamples.nf | 1 + modules/local/qiime2_filtertaxa.nf | 1 + modules/local/qiime2_inasv.nf | 2 ++ modules/local/qiime2_inseq.nf | 2 ++ modules/local/qiime2_intax.nf | 2 ++ modules/local/qiime2_intree.nf | 2 ++ modules/local/qiime2_train.nf | 1 + modules/local/qiime2_tree.nf | 1 + 23 files changed, 27 insertions(+) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index 273749ba..e4cb923f 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -24,6 +24,7 @@ process QIIME2_ALPHARAREFACTION { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 52c599c4..ce580997 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -25,6 +25,7 @@ process QIIME2_ANCOM_ASV { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime composition add-pseudocount \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index 3c065bb3..e5033d25 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -23,6 +23,7 @@ process QIIME2_ANCOM_TAX { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" mkdir ancom # Sum data at the specified level diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index a06100d4..73b6b13b 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -26,6 +26,7 @@ process QIIME2_BARPLOT { def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime taxa barplot \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index 96910c9a..e21c082c 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -24,6 +24,7 @@ process QIIME2_CLASSIFY { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime feature-classifier classify-sklearn \\ --i-classifier ${trained_classifier} \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 6b81f00e..967685b2 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -23,6 +23,7 @@ process QIIME2_DIVERSITY_ADONIS { def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime diversity adonis \\ --p-n-jobs $task.cpus \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index baebc03e..efe1d669 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -22,6 +22,7 @@ process QIIME2_DIVERSITY_ALPHA { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime diversity alpha-group-significance \\ --i-alpha-diversity ${core} \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 44df25f9..044acaa5 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -22,6 +22,7 @@ process QIIME2_DIVERSITY_BETA { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime diversity beta-group-significance \\ --i-distance-matrix ${core} \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index b29bd99e..ad7537b8 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -22,6 +22,7 @@ process QIIME2_DIVERSITY_BETAORD { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" mkdir beta_diversity qiime emperor plot \\ diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index 22235dfb..d248ae1a 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -32,6 +32,7 @@ process QIIME2_DIVERSITY_CORE { export UNIFRAC_USE_GPU=N export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 57c03a5e..9f70976b 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -30,6 +30,7 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" #produce raw count table in biom format "table/feature-table.biom" qiime tools export \\ diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 58e05b58..a8856728 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -21,6 +21,7 @@ process QIIME2_EXPORT_RELASV { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" #convert to relative abundances qiime feature-table relative-frequency \\ diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index c5b93d7c..50de8e5e 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -24,6 +24,7 @@ process QIIME2_EXPORT_RELTAX { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" ##on several taxa level array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max})) diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 6889befb..37c99989 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -23,6 +23,7 @@ process QIIME2_EXTRACT { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" ### Import qiime tools import \\ diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index d47ee14f..b6826132 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -22,6 +22,7 @@ process QIIME2_FEATURETABLE_GROUP { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime feature-table filter-samples \\ --i-table "${table}" \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 7f64e7e2..5bb4a2cf 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -24,6 +24,7 @@ process QIIME2_FILTERSAMPLES { def prefix = task.ext.prefix ?: "${filter}" """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime feature-table filter-samples \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 39cbb82c..0590f3fd 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -29,6 +29,7 @@ process QIIME2_FILTERTAXA { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" if ! [ \"${exclude_taxa}\" = \"none\" ]; then #filter sequences diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index d4848ba7..20fb526e 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -21,6 +21,8 @@ process QIIME2_INASV { script: """ + export MPLCONFIGDIR="\${PWD}/HOME" + # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 7c7c2007..7c966a61 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -21,6 +21,8 @@ process QIIME2_INSEQ { script: """ + export MPLCONFIGDIR="\${PWD}/HOME" + qiime tools import \\ --input-path "$seq" \\ --type 'FeatureData[Sequence]' \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index b9c3b039..6a208974 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -23,6 +23,8 @@ process QIIME2_INTAX { script: def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ + export MPLCONFIGDIR="\${PWD}/HOME" + $script_cmd qiime tools import \\ diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index a7a3ff3b..ec4e85d1 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -21,6 +21,8 @@ process QIIME2_INTREE { script: """ + export MPLCONFIGDIR="\${PWD}/HOME" + qiime tools import \\ --type 'Phylogeny[Rooted]' \\ --input-path $tree \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 4c4d69b2..892d510a 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -23,6 +23,7 @@ process QIIME2_TRAIN { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" #Train classifier qiime feature-classifier fit-classifier-naive-bayes \\ diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 6e7a89fe..99ef87b4 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -22,6 +22,7 @@ process QIIME2_TREE { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime alignment mafft \\ --i-sequences ${repseq} \\ From 8496c55948e7363504eb610ca34620a39d11bf4f Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 3 Nov 2023 15:05:00 +0100 Subject: [PATCH 03/17] change to tmp and export NUMBA_CACHE_DIR --- modules/local/qiime2_alphararefaction.nf | 5 +++-- modules/local/qiime2_ancom_asv.nf | 5 +++-- modules/local/qiime2_ancom_tax.nf | 5 +++-- modules/local/qiime2_barplot.nf | 5 +++-- modules/local/qiime2_classify.nf | 5 +++-- modules/local/qiime2_diversity_adonis.nf | 5 +++-- modules/local/qiime2_diversity_alpha.nf | 5 +++-- modules/local/qiime2_diversity_beta.nf | 5 +++-- modules/local/qiime2_diversity_betaord.nf | 5 +++-- modules/local/qiime2_diversity_core.nf | 5 +++-- modules/local/qiime2_export_absolute.nf | 5 +++-- modules/local/qiime2_export_relasv.nf | 5 +++-- modules/local/qiime2_export_reltax.nf | 5 +++-- modules/local/qiime2_extract.nf | 5 +++-- modules/local/qiime2_featuretable_group.nf | 5 +++-- modules/local/qiime2_filtersamples.nf | 5 +++-- modules/local/qiime2_filtertaxa.nf | 5 +++-- modules/local/qiime2_inasv.nf | 3 ++- modules/local/qiime2_inseq.nf | 3 ++- modules/local/qiime2_intax.nf | 3 ++- modules/local/qiime2_intree.nf | 3 ++- modules/local/qiime2_train.nf | 5 +++-- modules/local/qiime2_tree.nf | 5 +++-- 23 files changed, 65 insertions(+), 42 deletions(-) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index e4cb923f..b8c09557 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -23,8 +23,9 @@ process QIIME2_ALPHARAREFACTION { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index ce580997..1d5b7686 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -24,8 +24,9 @@ process QIIME2_ANCOM_ASV { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime composition add-pseudocount \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index e5033d25..f05be617 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -22,8 +22,9 @@ process QIIME2_ANCOM_TAX { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" mkdir ancom # Sum data at the specified level diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index 73b6b13b..d3c3feda 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -25,8 +25,9 @@ process QIIME2_BARPLOT { suffix = setting ? "_${table.baseName}" : "" def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime taxa barplot \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index e21c082c..be52e9bc 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -23,8 +23,9 @@ process QIIME2_CLASSIFY { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime feature-classifier classify-sklearn \\ --i-classifier ${trained_classifier} \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 967685b2..2b992219 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -22,8 +22,9 @@ process QIIME2_DIVERSITY_ADONIS { script: def args = task.ext.args ?: '' """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime diversity adonis \\ --p-n-jobs $task.cpus \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index efe1d669..4fb628dd 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -21,8 +21,9 @@ process QIIME2_DIVERSITY_ALPHA { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime diversity alpha-group-significance \\ --i-alpha-diversity ${core} \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 044acaa5..7ae8e551 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -21,8 +21,9 @@ process QIIME2_DIVERSITY_BETA { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime diversity beta-group-significance \\ --i-distance-matrix ${core} \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index ad7537b8..8852a9ce 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -21,8 +21,9 @@ process QIIME2_DIVERSITY_BETAORD { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" mkdir beta_diversity qiime emperor plot \\ diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index d248ae1a..7c104cfa 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -31,8 +31,9 @@ process QIIME2_DIVERSITY_CORE { # COMMENT: might be fixed in version after QIIME2 2023.5 export UNIFRAC_USE_GPU=N - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 9f70976b..e96968ec 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -29,8 +29,9 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" #produce raw count table in biom format "table/feature-table.biom" qiime tools export \\ diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index a8856728..697d53a3 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -20,8 +20,9 @@ process QIIME2_EXPORT_RELASV { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" #convert to relative abundances qiime feature-table relative-frequency \\ diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index 50de8e5e..a70f0579 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -23,8 +23,9 @@ process QIIME2_EXPORT_RELTAX { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" ##on several taxa level array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max})) diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 37c99989..d9bb373c 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -22,8 +22,9 @@ process QIIME2_EXTRACT { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" ### Import qiime tools import \\ diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index b6826132..b2346517 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -21,8 +21,9 @@ process QIIME2_FEATURETABLE_GROUP { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime feature-table filter-samples \\ --i-table "${table}" \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 5bb4a2cf..6a69c2e8 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -23,8 +23,9 @@ process QIIME2_FILTERSAMPLES { def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'" def prefix = task.ext.prefix ?: "${filter}" """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime feature-table filter-samples \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 0590f3fd..df11ec08 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -28,8 +28,9 @@ process QIIME2_FILTERTAXA { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" if ! [ \"${exclude_taxa}\" = \"none\" ]; then #filter sequences diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index 20fb526e..0fc2d2c5 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -21,7 +21,8 @@ process QIIME2_INASV { script: """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 7c966a61..1aabf290 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -21,7 +21,8 @@ process QIIME2_INSEQ { script: """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime tools import \\ --input-path "$seq" \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index 6a208974..e2ef1ab8 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -23,7 +23,8 @@ process QIIME2_INTAX { script: def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" $script_cmd diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index ec4e85d1..6ee72a7c 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -21,7 +21,8 @@ process QIIME2_INTREE { script: """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime tools import \\ --type 'Phylogeny[Rooted]' \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 892d510a..757fedf2 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -22,8 +22,9 @@ process QIIME2_TRAIN { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" #Train classifier qiime feature-classifier fit-classifier-naive-bayes \\ diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 99ef87b4..c636af76 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -21,8 +21,9 @@ process QIIME2_TREE { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime alignment mafft \\ --i-sequences ${repseq} \\ From ac61247d67ba249783cf2942781d2d12e132448b Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 10:28:23 +0100 Subject: [PATCH 04/17] place XDG_CONFIG_HOME, MPLCONFIGDIR, NUMBA_CACHE_DIR in work directory instead of /tmp/ --- modules/local/qiime2_alphararefaction.nf | 6 +++--- modules/local/qiime2_ancom_asv.nf | 6 +++--- modules/local/qiime2_ancom_tax.nf | 6 +++--- modules/local/qiime2_barplot.nf | 6 +++--- modules/local/qiime2_classify.nf | 6 +++--- modules/local/qiime2_diversity_adonis.nf | 6 +++--- modules/local/qiime2_diversity_alpha.nf | 6 +++--- modules/local/qiime2_diversity_beta.nf | 6 +++--- modules/local/qiime2_diversity_betaord.nf | 6 +++--- modules/local/qiime2_diversity_core.nf | 6 +++--- modules/local/qiime2_export_absolute.nf | 6 +++--- modules/local/qiime2_export_relasv.nf | 6 +++--- modules/local/qiime2_export_reltax.nf | 6 +++--- modules/local/qiime2_extract.nf | 6 +++--- modules/local/qiime2_featuretable_group.nf | 6 +++--- modules/local/qiime2_filtersamples.nf | 6 +++--- modules/local/qiime2_filtertaxa.nf | 6 +++--- modules/local/qiime2_inasv.nf | 4 ++-- modules/local/qiime2_inseq.nf | 4 ++-- modules/local/qiime2_intax.nf | 4 ++-- modules/local/qiime2_intree.nf | 4 ++-- modules/local/qiime2_train.nf | 6 +++--- modules/local/qiime2_tree.nf | 6 +++--- 23 files changed, 65 insertions(+), 65 deletions(-) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index b8c09557..8ed0cc13 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -23,9 +23,9 @@ process QIIME2_ALPHARAREFACTION { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 1d5b7686..39e31e8d 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -24,9 +24,9 @@ process QIIME2_ANCOM_ASV { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime composition add-pseudocount \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index f05be617..ecaf2a1d 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -22,9 +22,9 @@ process QIIME2_ANCOM_TAX { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" mkdir ancom # Sum data at the specified level diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index d3c3feda..cbb933c6 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -25,9 +25,9 @@ process QIIME2_BARPLOT { suffix = setting ? "_${table.baseName}" : "" def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime taxa barplot \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index be52e9bc..414f515b 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -23,9 +23,9 @@ process QIIME2_CLASSIFY { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime feature-classifier classify-sklearn \\ --i-classifier ${trained_classifier} \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 2b992219..7fbef538 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -22,9 +22,9 @@ process QIIME2_DIVERSITY_ADONIS { script: def args = task.ext.args ?: '' """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime diversity adonis \\ --p-n-jobs $task.cpus \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index 4fb628dd..ab9b2440 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -21,9 +21,9 @@ process QIIME2_DIVERSITY_ALPHA { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime diversity alpha-group-significance \\ --i-alpha-diversity ${core} \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 7ae8e551..97f6c6ae 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -21,9 +21,9 @@ process QIIME2_DIVERSITY_BETA { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime diversity beta-group-significance \\ --i-distance-matrix ${core} \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index 8852a9ce..59b7e6f6 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -21,9 +21,9 @@ process QIIME2_DIVERSITY_BETAORD { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" mkdir beta_diversity qiime emperor plot \\ diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index 7c104cfa..f3a775b3 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -31,9 +31,9 @@ process QIIME2_DIVERSITY_CORE { # COMMENT: might be fixed in version after QIIME2 2023.5 export UNIFRAC_USE_GPU=N - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index e96968ec..9f7d9d11 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -29,9 +29,9 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" #produce raw count table in biom format "table/feature-table.biom" qiime tools export \\ diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 697d53a3..65a6add5 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -20,9 +20,9 @@ process QIIME2_EXPORT_RELASV { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" #convert to relative abundances qiime feature-table relative-frequency \\ diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index a70f0579..32ea7d2d 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -23,9 +23,9 @@ process QIIME2_EXPORT_RELTAX { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" ##on several taxa level array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max})) diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index d9bb373c..4b8a60b7 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -22,9 +22,9 @@ process QIIME2_EXTRACT { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" ### Import qiime tools import \\ diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index b2346517..887a1e75 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -21,9 +21,9 @@ process QIIME2_FEATURETABLE_GROUP { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ --i-table "${table}" \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 6a69c2e8..c9b279ef 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -23,9 +23,9 @@ process QIIME2_FILTERSAMPLES { def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'" def prefix = task.ext.prefix ?: "${filter}" """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index df11ec08..66013279 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -28,9 +28,9 @@ process QIIME2_FILTERTAXA { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" if ! [ \"${exclude_taxa}\" = \"none\" ]; then #filter sequences diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index 0fc2d2c5..68c08d58 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -21,8 +21,8 @@ process QIIME2_INASV { script: """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 1aabf290..a11529a3 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -21,8 +21,8 @@ process QIIME2_INSEQ { script: """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime tools import \\ --input-path "$seq" \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index e2ef1ab8..cb7e7269 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -23,8 +23,8 @@ process QIIME2_INTAX { script: def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" $script_cmd diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index 6ee72a7c..817e2a7b 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -21,8 +21,8 @@ process QIIME2_INTREE { script: """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime tools import \\ --type 'Phylogeny[Rooted]' \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 757fedf2..09c70735 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -22,9 +22,9 @@ process QIIME2_TRAIN { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" #Train classifier qiime feature-classifier fit-classifier-naive-bayes \\ diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index c636af76..26711b04 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -21,9 +21,9 @@ process QIIME2_TREE { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime alignment mafft \\ --i-sequences ${repseq} \\ From b6b7928185617ae2d1229a9fa1934eff9c748143 Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 13:54:07 +0100 Subject: [PATCH 05/17] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddb0e72c..0fa237ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#655](https://github.com/nf-core/ampliseq/pull/655) - Added `NUMBA_CACHE_DIR` to fix downstream analysis with QIIME2 that failed on some systems + ### `Dependencies` ### `Removed` From ac8b05c97d55f6996777d95f3083f86c39e4654e Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 14:00:47 +0100 Subject: [PATCH 06/17] replace tab with 4 spaces --- modules/local/qiime2_alphararefaction.nf | 2 +- modules/local/qiime2_ancom_asv.nf | 2 +- modules/local/qiime2_ancom_tax.nf | 2 +- modules/local/qiime2_barplot.nf | 2 +- modules/local/qiime2_classify.nf | 2 +- modules/local/qiime2_diversity_adonis.nf | 2 +- modules/local/qiime2_diversity_alpha.nf | 2 +- modules/local/qiime2_diversity_beta.nf | 2 +- modules/local/qiime2_diversity_betaord.nf | 2 +- modules/local/qiime2_diversity_core.nf | 2 +- modules/local/qiime2_export_absolute.nf | 2 +- modules/local/qiime2_export_relasv.nf | 2 +- modules/local/qiime2_export_reltax.nf | 2 +- modules/local/qiime2_extract.nf | 2 +- modules/local/qiime2_featuretable_group.nf | 2 +- modules/local/qiime2_filtersamples.nf | 2 +- modules/local/qiime2_filtertaxa.nf | 2 +- modules/local/qiime2_train.nf | 2 +- modules/local/qiime2_tree.nf | 2 +- subworkflows/local/dada2_taxonomy_wf.nf | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index 8ed0cc13..c37a8d57 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -24,7 +24,7 @@ process QIIME2_ALPHARAREFACTION { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 39e31e8d..c5ee19a3 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -25,7 +25,7 @@ process QIIME2_ANCOM_ASV { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime composition add-pseudocount \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index ecaf2a1d..1c5eccc8 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -23,7 +23,7 @@ process QIIME2_ANCOM_TAX { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" mkdir ancom diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index cbb933c6..cea39171 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -26,7 +26,7 @@ process QIIME2_BARPLOT { def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime taxa barplot \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index 414f515b..a84bde40 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -24,7 +24,7 @@ process QIIME2_CLASSIFY { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime feature-classifier classify-sklearn \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 7fbef538..23016923 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -23,7 +23,7 @@ process QIIME2_DIVERSITY_ADONIS { def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime diversity adonis \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index ab9b2440..5062b74b 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_ALPHA { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime diversity alpha-group-significance \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 97f6c6ae..2e0d5864 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_BETA { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime diversity beta-group-significance \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index 59b7e6f6..ad6d8266 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_BETAORD { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" mkdir beta_diversity diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index f3a775b3..d0569d87 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -32,7 +32,7 @@ process QIIME2_DIVERSITY_CORE { export UNIFRAC_USE_GPU=N export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 9f7d9d11..5e217f4a 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -30,7 +30,7 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" #produce raw count table in biom format "table/feature-table.biom" diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 65a6add5..85eedcda 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -21,7 +21,7 @@ process QIIME2_EXPORT_RELASV { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" #convert to relative abundances diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index 32ea7d2d..4b287917 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -24,7 +24,7 @@ process QIIME2_EXPORT_RELTAX { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" ##on several taxa level diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 4b8a60b7..9e4bf2fa 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -23,7 +23,7 @@ process QIIME2_EXTRACT { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" ### Import diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index 887a1e75..eacb4d61 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -22,7 +22,7 @@ process QIIME2_FEATURETABLE_GROUP { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index c9b279ef..01c9c11a 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -24,7 +24,7 @@ process QIIME2_FILTERSAMPLES { def prefix = task.ext.prefix ?: "${filter}" """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 66013279..3ea8828e 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -29,7 +29,7 @@ process QIIME2_FILTERTAXA { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" if ! [ \"${exclude_taxa}\" = \"none\" ]; then diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 09c70735..48174e3c 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -23,7 +23,7 @@ process QIIME2_TRAIN { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" #Train classifier diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 26711b04..a595b64a 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -22,7 +22,7 @@ process QIIME2_TREE { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime alignment mafft \\ diff --git a/subworkflows/local/dada2_taxonomy_wf.nf b/subworkflows/local/dada2_taxonomy_wf.nf index 9673b45e..c0e5a85d 100644 --- a/subworkflows/local/dada2_taxonomy_wf.nf +++ b/subworkflows/local/dada2_taxonomy_wf.nf @@ -83,7 +83,7 @@ workflow DADA2_TAXONOMY_WF { //set file name prefix for SH assignments if (!params.skip_dada_addspecies) { ASV_SH_name = "ASV_tax_species_SH" - } else { + } else { ASV_SH_name = "ASV_tax_SH" } //find SHs From 2326b7ef4ab9c5cc01924eeb00f94ee2cc820f79 Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 14:44:57 +0100 Subject: [PATCH 07/17] move conda check to script section --- CHANGELOG.md | 2 ++ modules/local/qiime2_alphararefaction.nf | 9 ++++----- modules/local/qiime2_ancom_asv.nf | 9 ++++----- modules/local/qiime2_ancom_tax.nf | 9 ++++----- modules/local/qiime2_barplot.nf | 9 ++++----- modules/local/qiime2_classify.nf | 9 ++++----- modules/local/qiime2_diversity_adonis.nf | 9 ++++----- modules/local/qiime2_diversity_alpha.nf | 9 ++++----- modules/local/qiime2_diversity_beta.nf | 9 ++++----- modules/local/qiime2_diversity_betaord.nf | 9 ++++----- modules/local/qiime2_diversity_core.nf | 9 ++++----- modules/local/qiime2_export_absolute.nf | 9 ++++----- modules/local/qiime2_export_relasv.nf | 9 ++++----- modules/local/qiime2_export_reltax.nf | 9 ++++----- modules/local/qiime2_extract.nf | 9 ++++----- modules/local/qiime2_featuretable_group.nf | 9 ++++----- modules/local/qiime2_filtersamples.nf | 9 ++++----- modules/local/qiime2_filtertaxa.nf | 9 ++++----- modules/local/qiime2_inasv.nf | 9 ++++----- modules/local/qiime2_inseq.nf | 9 ++++----- modules/local/qiime2_intax.nf | 9 ++++----- modules/local/qiime2_intree.nf | 9 ++++----- modules/local/qiime2_train.nf | 9 ++++----- modules/local/qiime2_tree.nf | 9 ++++----- 24 files changed, 94 insertions(+), 115 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddb0e72c..c9381a95 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#656](https://github.com/nf-core/ampliseq/pull/656) - Moved conda-check to script-section and replaced `exit 1` with `error()` + ### `Dependencies` ### `Removed` diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index 273749ba..44319b94 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -3,11 +3,6 @@ process QIIME2_ALPHARAREFACTION { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(metadata) path(table) @@ -22,6 +17,10 @@ process QIIME2_ALPHARAREFACTION { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 52c599c4..54ccd6c4 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -7,11 +7,6 @@ process QIIME2_ANCOM_ASV { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(table) @@ -23,6 +18,10 @@ process QIIME2_ANCOM_ASV { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index 3c065bb3..91567c0e 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -5,11 +5,6 @@ process QIIME2_ANCOM_TAX { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(table), path(taxonomy) ,val(taxlevel) @@ -21,6 +16,10 @@ process QIIME2_ANCOM_TAX { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" mkdir ancom diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index a06100d4..d66ef4ee 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -3,11 +3,6 @@ process QIIME2_BARPLOT { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(metadata) path(table) @@ -22,6 +17,10 @@ process QIIME2_BARPLOT { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } suffix = setting ? "_${table.baseName}" : "" def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index 96910c9a..d7cf1929 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -4,11 +4,6 @@ process QIIME2_CLASSIFY { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(trained_classifier) path(repseq) @@ -22,6 +17,10 @@ process QIIME2_CLASSIFY { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 6b81f00e..24b7afe8 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_ADONIS { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(core), val(formula) @@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_ADONIS { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index baebc03e..237c9664 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_ALPHA { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(core) @@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_ALPHA { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 44df25f9..dbc6cd18 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_BETA { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(core), val(category) @@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_BETA { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index b29bd99e..3c199740 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_BETAORD { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(core) @@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_BETAORD { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" mkdir beta_diversity diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index 22235dfb..c1866ead 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -3,11 +3,6 @@ process QIIME2_DIVERSITY_CORE { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(metadata) path(table) @@ -26,6 +21,10 @@ process QIIME2_DIVERSITY_CORE { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ # FIX: detecting a viable GPU on your system, but the GPU is unavailable for compute, causing UniFrac to fail. # COMMENT: might be fixed in version after QIIME2 2023.5 diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 57c03a5e..75fe7f09 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -3,11 +3,6 @@ process QIIME2_EXPORT_ABSOLUTE { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(table) path(repseq) @@ -28,6 +23,10 @@ process QIIME2_EXPORT_ABSOLUTE { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 58e05b58..c9e0b139 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -3,11 +3,6 @@ process QIIME2_EXPORT_RELASV { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(table) @@ -19,6 +14,10 @@ process QIIME2_EXPORT_RELASV { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index c5b93d7c..f8849ed3 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -3,11 +3,6 @@ process QIIME2_EXPORT_RELTAX { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(table) path(taxonomy) @@ -22,6 +17,10 @@ process QIIME2_EXPORT_RELTAX { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 6889befb..3ba5a99c 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -5,11 +5,6 @@ process QIIME2_EXTRACT { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple val(meta), path(database) @@ -21,6 +16,10 @@ process QIIME2_EXTRACT { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index d47ee14f..11f74f94 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -4,11 +4,6 @@ process QIIME2_FEATURETABLE_GROUP { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(table), path(metadata), val(category) @@ -20,6 +15,10 @@ process QIIME2_FEATURETABLE_GROUP { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 7f64e7e2..c4bad400 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -4,11 +4,6 @@ process QIIME2_FILTERSAMPLES { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple path(metadata), path(table), val(filter) @@ -20,6 +15,10 @@ process QIIME2_FILTERSAMPLES { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'" def prefix = task.ext.prefix ?: "${filter}" """ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 39cbb82c..4ffb0fa9 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -4,11 +4,6 @@ process QIIME2_FILTERTAXA { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(table) path(repseq) @@ -27,6 +22,10 @@ process QIIME2_FILTERTAXA { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index d4848ba7..28a44821 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -4,11 +4,6 @@ process QIIME2_INASV { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(asv) @@ -20,6 +15,10 @@ process QIIME2_INASV { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 7c7c2007..fbb3eecb 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -4,11 +4,6 @@ process QIIME2_INSEQ { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(seq) @@ -20,6 +15,10 @@ process QIIME2_INSEQ { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ qiime tools import \\ --input-path "$seq" \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index b9c3b039..42715945 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -4,11 +4,6 @@ process QIIME2_INTAX { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(tax) //ASV_tax_species.tsv val(script) @@ -21,6 +16,10 @@ process QIIME2_INTAX { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ $script_cmd diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index a7a3ff3b..3e13879c 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -4,11 +4,6 @@ process QIIME2_INTREE { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple val(meta), path(tree) @@ -20,6 +15,10 @@ process QIIME2_INTREE { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ qiime tools import \\ --type 'Phylogeny[Rooted]' \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 4c4d69b2..d07945c8 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -5,11 +5,6 @@ process QIIME2_TRAIN { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple val(meta), path(qza) @@ -21,6 +16,10 @@ process QIIME2_TRAIN { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 6e7a89fe..89f30f60 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -3,11 +3,6 @@ process QIIME2_TREE { container "qiime2/core:2023.7" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: path(repseq) @@ -20,6 +15,10 @@ process QIIME2_TREE { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="\${PWD}/HOME" From ba9b433e77a79f5c1dc2db5df1d3d7abddbeaeec Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 9 Nov 2023 14:17:43 +0100 Subject: [PATCH 08/17] fix QIIME2 taxonomy reporting --- assets/report_template.Rmd | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd index f0b4073e..7c4e242a 100644 --- a/assets/report_template.Rmd +++ b/assets/report_template.Rmd @@ -989,17 +989,18 @@ asv_tax <- read.table(params$qiime2_taxonomy, header = TRUE, sep = "\t") asv_tax <- subset(asv_tax, select = Taxon) # Remove greengenes85 ".__" placeholders -df = as.data.frame(lapply(asv_tax, function(x) gsub(".__", "", x))) -# remove all last, empty ; -df = as.data.frame(lapply(df, function(x) gsub(" ;","",x))) +df = as.data.frame(lapply(asv_tax, function(x) gsub(" .__", "", x))) +# remove all empty ; +df = as.data.frame(lapply(df, function(x) gsub(";;","",x))) # remove last remaining, empty ; -df = as.data.frame(lapply(df, function(x) gsub("; $","",x))) +df = as.data.frame(lapply(df, function(x) gsub(";$","",x))) # get maximum amount of taxa levels per ASV -max_taxa <- lengths(regmatches(df$Taxon, gregexpr("; ", df$Taxon)))+1 +max_taxa <- lengths(regmatches(df$Taxon, gregexpr(";", df$Taxon)))+1 -# Currently, all QIIME2 databases seem to have the same levels! +# Currently, all QIIME2 databases seem to have the same levels! But for compatibility, restrict number of levels to max_taxa level <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species") +level <- head(level, n= max(max_taxa) ) # Calculate the classified numbers/percent of asv n_asv_tax = nrow(asv_tax) From 0db5905c8a3aae066aed14f5f650a2597ad7101d Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 9 Nov 2023 14:42:35 +0100 Subject: [PATCH 09/17] fix length filter reporting --- assets/report_template.Rmd | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd index 7c4e242a..6dff7817 100644 --- a/assets/report_template.Rmd +++ b/assets/report_template.Rmd @@ -724,9 +724,10 @@ if ( params$max_len_asv != 0 ) { } # replace 1 with 1.5 to display on log scale -filter_len_profile$Counts[filter_len_profile$Counts == 1] <- 1.5 +filter_len_profile_replaced <- filter_len_profile +filter_len_profile_replaced$Counts[filter_len_profile_replaced$Counts == 1] <- 1.5 -plot_filter_len_profile <- ggplot(filter_len_profile, +plot_filter_len_profile <- ggplot(filter_len_profile_replaced, aes(x = Length, y = Counts)) + geom_bar(stat = "identity", fill = rgb(0.1, 0.4, 0.75), width = 0.5) + ylab("Number of ASVs") + From e803b525eab49bee6ffdeba34c6b360076ddaf25 Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 9 Nov 2023 14:48:47 +0100 Subject: [PATCH 10/17] params docs: clarify --input_folder --- nextflow_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 9652e68b..41427472 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -98,15 +98,15 @@ }, "multiple_sequencing_runs": { "type": "boolean", - "description": "If samples were sequenced in multiple sequencing runs", - "help_text": "Expects one sub-folder per sequencing run in the folder specified by `--input` containing sequencing data of the specific run.\nSample identifiers are taken from sequencing files, specifically the string before the first underscore will be the sample ID. Sample IDs across all sequencing runs (all sequencing files) have to be unique. If this is not the case, please use a sample sheet as input instead.\n\nExample for input data organization:\n\n```bash\ndata\n |-run1\n | |-sample1_1_L001_R1_001.fastq.gz\n | |-sample1_1_L001_R2_001.fastq.gz\n | |-sample2_1_L001_R1_001.fastq.gz\n | |-sample2_1_L001_R2_001.fastq.gz\n |\n |-run2\n |-sample3_1_L001_R1_001.fastq.gz\n |-sample3_1_L001_R2_001.fastq.gz\n |-sample4_1_L001_R1_001.fastq.gz\n |-sample4_1_L001_R2_001.fastq.gz\n```\n\nExample command to analyze this data in one pipeline run:\n\n```bash\nnextflow run nf-core/ampliseq \\\n -profile singularity \\\n --input \"data\" \\\n --FW_primer \"GTGYCAGCMGCCGCGGTAA\" \\\n --RV_primer \"GGACTACNVGGGTWTCTAAT\" \\\n --metadata \"data/Metadata.tsv\" \\\n --multiple_sequencing_runs\n```", + "description": "If using `--input_folder`: samples were sequenced in multiple sequencing runs", + "help_text": "Expects one sub-folder per sequencing run in the folder specified by `--input_folder` containing sequencing data of the specific run.\nSample identifiers are taken from sequencing files, specifically the string before the first underscore will be the sample ID. Sample IDs across all sequencing runs (all sequencing files) have to be unique. If this is not the case, please use a sample sheet as input instead.\n\nExample for input data organization:\n\n```bash\ndata\n |-run1\n | |-sample1_1_L001_R1_001.fastq.gz\n | |-sample1_1_L001_R2_001.fastq.gz\n | |-sample2_1_L001_R1_001.fastq.gz\n | |-sample2_1_L001_R2_001.fastq.gz\n |\n |-run2\n |-sample3_1_L001_R1_001.fastq.gz\n |-sample3_1_L001_R2_001.fastq.gz\n |-sample4_1_L001_R1_001.fastq.gz\n |-sample4_1_L001_R2_001.fastq.gz\n```\n\nExample command to analyze this data in one pipeline run:\n\n```bash\nnextflow run nf-core/ampliseq \\\n -profile singularity \\\n --input_folder \"data\" \\\n --FW_primer \"GTGYCAGCMGCCGCGGTAA\" \\\n --RV_primer \"GGACTACNVGGGTWTCTAAT\" \\\n --metadata \"data/Metadata.tsv\" \\\n --multiple_sequencing_runs\n```", "fa_icon": "fas fa-running" }, "extension": { "type": "string", "default": "/*_R{1,2}_001.fastq.gz", - "description": "Naming of sequencing files", - "help_text": "Indicates the naming of sequencing files (default: `\"/*_R{1,2}_001.fastq.gz\"`).\n\nPlease note:\n\n1. The prepended slash (`/`) is required\n2. The star (`*`) is the required wildcard for sample names\n3. The curly brackets (`{}`) enclose the orientation for paired end reads, separated by a comma (`,`).\n4. The pattern must be enclosed in quotes\n\nFor example for one sample (name: `1`) with forward (file: `1_a.fastq.gz`) and reverse (file: `1_b.fastq.gz`) reads in folder `data`:\n\n```bash\n--input \"data\" --extension \"/*_{a,b}.fastq.gz\"\n```" + "description": "If using `--input_folder`: naming of sequencing files", + "help_text": "Indicates the naming of sequencing files (default: `\"/*_R{1,2}_001.fastq.gz\"`).\n\nPlease note:\n\n1. The prepended slash (`/`) is required\n2. The star (`*`) is the required wildcard for sample names\n3. The curly brackets (`{}`) enclose the orientation for paired end reads, separated by a comma (`,`).\n4. The pattern must be enclosed in quotes\n\nFor example for one sample (name: `1`) with forward (file: `1_a.fastq.gz`) and reverse (file: `1_b.fastq.gz`) reads in folder `data`:\n\n```bash\n--input_folder \"data\" --extension \"/*_{a,b}.fastq.gz\"\n```" }, "min_read_counts": { "type": "integer", From 29ddd75d5262ce1ec11f177edfa078f998270c90 Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 9 Nov 2023 15:39:16 +0100 Subject: [PATCH 11/17] params docs: re-ordering and symbols --- nextflow_schema.json | 208 ++++++++++++++++++++++++------------------- 1 file changed, 116 insertions(+), 92 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 41427472..1d3098da 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -76,25 +76,30 @@ "properties": { "illumina_novaseq": { "type": "boolean", - "description": "If data has binned quality scores such as Illumina NovaSeq" + "description": "If data has binned quality scores such as Illumina NovaSeq", + "fa_icon": "fas fa-align-justify" }, "pacbio": { "type": "boolean", - "description": "If data is single-ended PacBio reads instead of Illumina" + "description": "If data is single-ended PacBio reads instead of Illumina", + "fa_icon": "fas fa-align-justify" }, "iontorrent": { "type": "boolean", - "description": "If data is single-ended IonTorrent reads instead of Illumina" + "description": "If data is single-ended IonTorrent reads instead of Illumina", + "fa_icon": "fas fa-align-justify" }, "single_end": { "type": "boolean", "description": "If data is single-ended Illumina reads instead of paired-end", - "help_text": "When using a sample sheet with `--input` containing forward and reverse reads, specifying `--single_end` will only extract forward reads and treat the data as single ended instead of extracting forward and reverse reads." + "help_text": "When using a sample sheet with `--input` containing forward and reverse reads, specifying `--single_end` will only extract forward reads and treat the data as single ended instead of extracting forward and reverse reads.", + "fa_icon": "fas fa-align-left" }, "illumina_pe_its": { "type": "boolean", "description": "If analysing ITS amplicons or any other region with large length variability with Illumina paired end reads", - "help_text": "This will cause the pipeline to\n- not truncate input reads if not `--trunclenf` and `--trunclenr` are overwriting defaults\n- remove reverse complement primers from the end of reads in case the read length exceeds the amplicon length" + "help_text": "This will cause the pipeline to\n- not truncate input reads if not `--trunclenf` and `--trunclenr` are overwriting defaults\n- remove reverse complement primers from the end of reads in case the read length exceeds the amplicon length", + "fa_icon": "fas fa-align-justify" }, "multiple_sequencing_runs": { "type": "boolean", @@ -106,7 +111,8 @@ "type": "string", "default": "/*_R{1,2}_001.fastq.gz", "description": "If using `--input_folder`: naming of sequencing files", - "help_text": "Indicates the naming of sequencing files (default: `\"/*_R{1,2}_001.fastq.gz\"`).\n\nPlease note:\n\n1. The prepended slash (`/`) is required\n2. The star (`*`) is the required wildcard for sample names\n3. The curly brackets (`{}`) enclose the orientation for paired end reads, separated by a comma (`,`).\n4. The pattern must be enclosed in quotes\n\nFor example for one sample (name: `1`) with forward (file: `1_a.fastq.gz`) and reverse (file: `1_b.fastq.gz`) reads in folder `data`:\n\n```bash\n--input_folder \"data\" --extension \"/*_{a,b}.fastq.gz\"\n```" + "help_text": "Indicates the naming of sequencing files (default: `\"/*_R{1,2}_001.fastq.gz\"`).\n\nPlease note:\n\n1. The prepended slash (`/`) is required\n2. The star (`*`) is the required wildcard for sample names\n3. The curly brackets (`{}`) enclose the orientation for paired end reads, separated by a comma (`,`).\n4. The pattern must be enclosed in quotes\n\nFor example for one sample (name: `1`) with forward (file: `1_a.fastq.gz`) and reverse (file: `1_b.fastq.gz`) reads in folder `data`:\n\n```bash\n--input_folder \"data\" --extension \"/*_{a,b}.fastq.gz\"\n```", + "fa_icon": "fab fa-amilia" }, "min_read_counts": { "type": "integer", @@ -118,14 +124,15 @@ "ignore_empty_input_files": { "type": "boolean", "description": "Ignore input files with too few reads.", - "help_text": "Ignore input files with less reads than specified by `--min_read_counts` and continue the pipeline without those samples." + "help_text": "Ignore input files with less reads than specified by `--min_read_counts` and continue the pipeline without those samples.", + "fa_icon": "fas fa-arrow-right" } - } + }, + "fa_icon": "fas fa-align-justify" }, "primer_removal": { "title": "Primer removal", "type": "object", - "description": "", "default": "", "properties": { "retain_untrimmed": { @@ -137,12 +144,14 @@ "cutadapt_min_overlap": { "type": "integer", "default": 3, - "description": "Sets the minimum overlap for valid matches of primer sequences with reads for cutadapt (-O)." + "description": "Sets the minimum overlap for valid matches of primer sequences with reads for cutadapt (-O).", + "fa_icon": "fas fa-align-left" }, "cutadapt_max_error_rate": { "type": "number", "default": 0.1, - "description": "Sets the maximum error rate for valid matches of primer sequences with reads for cutadapt (-e)." + "description": "Sets the maximum error rate for valid matches of primer sequences with reads for cutadapt (-e).", + "fa_icon": "fas fa-exclamation-circle" }, "double_primer": { "type": "boolean", @@ -153,9 +162,11 @@ "ignore_failed_trimming": { "type": "boolean", "description": "Ignore files with too few reads after trimming.", - "help_text": "Ignore files with less reads than specified by `--min_read_counts` after trimming and continue the pipeline without those samples." + "help_text": "Ignore files with less reads than specified by `--min_read_counts` after trimming and continue the pipeline without those samples.", + "fa_icon": "fas fa-arrow-right" } - } + }, + "fa_icon": "fas fa-align-left" }, "read_trimming_and_quality_filtering": { "title": "Read trimming and quality filtering", @@ -188,7 +199,8 @@ "description": "Assures that values chosen with --trunc_qmin will retain a fraction of reads.", "help_text": "Value can range from 0 to 1. 0 means no reads need to be retained and 1 means all reads need to be retained. The minimum lengths of --trunc_qmin and --trunc_rmin are chosen as DADA2 cutoffs.", "minimum": 0, - "maximum": 1 + "maximum": 1, + "fa_icon": "fas fa-greater-than-equal" }, "max_ee": { "type": "integer", @@ -213,14 +225,15 @@ "ignore_failed_filtering": { "type": "boolean", "description": "Ignore files with too few reads after quality filtering.", - "help_text": "Ignore files with fewer reads than specified by `--min_read_counts` after trimming and continue the pipeline without those samples. Please review all quality trimming and filtering options before using this parameter. For example, one sample with shorter sequences than other samples might loose all sequences due to minimum length requirements by read truncation (see --trunclenf)." + "help_text": "Ignore files with fewer reads than specified by `--min_read_counts` after trimming and continue the pipeline without those samples. Please review all quality trimming and filtering options before using this parameter. For example, one sample with shorter sequences than other samples might loose all sequences due to minimum length requirements by read truncation (see --trunclenf).", + "fa_icon": "fas fa-arrow-right" } - } + }, + "fa_icon": "fas fa-ban" }, "amplicon_sequence_variants_asv_calculation": { "title": "Amplicon Sequence Variants (ASV) calculation", "type": "object", - "description": "", "default": "", "properties": { "sample_inference": { @@ -235,12 +248,85 @@ "description": "Not recommended: When paired end reads are not sufficiently overlapping for merging.", "help_text": "This parameters specifies that paired-end reads are not merged after denoising but concatenated (separated by 10 N's). This is of advantage when an amplicon was sequenced that is too long for merging (i.e. bad experimental design). This is an alternative to only analyzing the forward or reverse read in case of non-overlapping paired-end sequencing data.\n\n**This parameter is not recommended! Only if all other options fail.**" } - } + }, + "fa_icon": "fas fa-braille" + }, + "asv_post_processing": { + "title": "ASV post processing", + "type": "object", + "default": "", + "properties": { + "vsearch_cluster": { + "type": "boolean", + "description": "Post-cluster ASVs with VSEARCH", + "help_text": "ASVs will be clustered with VSEARCH using the id value found in `--vsearch_cluster_id`." + }, + "vsearch_cluster_id": { + "type": "number", + "default": 0.97, + "minimum": 0, + "maximum": 1, + "description": "Pairwise Identity value used when post-clustering ASVs if `--vsearch_cluster` option is used (default: 0.97).", + "help_text": "Lowering or increasing this value can change the number ASVs left over after clustering." + }, + "filter_ssu": { + "type": "string", + "description": "Enable SSU filtering. Comma separated list of kingdoms (domains) in Barrnap, a combination (or one) of \"bac\", \"arc\", \"mito\", and \"euk\". ASVs that have their lowest evalue in that kingdoms are kept.", + "enum": [ + "bac,arc,mito,euk", + "bac", + "arc", + "mito", + "euk", + "bac,arc", + "bac,mito", + "bac,euk", + "arc,mito", + "arc,euk", + "mito,euk", + "bac,arc,mito", + "bac,mito,euk", + "arc,mito,euk" + ] + }, + "min_len_asv": { + "type": "integer", + "description": "Minimal ASV length", + "help_text": "Remove ASV that are below the minimum length threshold (default: filter is disabled, otherwise 1). Increasing the threshold might reduce false positive ASVs (e.g. PCR off-targets)." + }, + "max_len_asv": { + "type": "integer", + "description": "Maximum ASV length", + "help_text": "Remove ASV that are above the maximum length threshold (default: filter is disabled, otherwise 1000000). Lowering the threshold might reduce false positive ASVs (e.g. PCR off-targets)." + }, + "filter_codons": { + "type": "boolean", + "description": "Filter ASVs based on codon usage", + "help_text": "ASVs will be filtered to contain no stop codon in their coding sequence and that their length is a multiple of 3." + }, + "orf_start": { + "type": "integer", + "default": 1, + "description": "Starting position of codon tripletts", + "help_text": "By default, when `--filter_codons` is set, the codons start from the first position of the ASV sequences. The start of the codons can be changed to any position." + }, + "orf_end": { + "type": "integer", + "description": "Ending position of codon tripletts", + "help_text": "By default, when `--filter_codons` is set, the codons are checked until the end of the ASV sequences. If you would like to change this setting, you can specify until which position of the ASV sequences the codon triplets are checked.\n\nPlease note that the length of the ASV from the beginning or from the `--orf_start` until this position must be a multiple of 3." + }, + "stop_codons": { + "type": "string", + "default": "TAA,TAG", + "description": "Define stop codons", + "help_text": "By default, when `--filter_codons` is set, the codons `TAA,TAG` are set as stop codons. Here you can specify any comma-separated list of codons to be used as stop codons, e.g. `--stop_codons \"TAA,TAG,TGA\"`" + } + }, + "fa_icon": "fas fa-filter" }, "taxonomic_database": { "title": "Taxonomic database", "type": "object", - "description": "", "default": "", "properties": { "dada_ref_taxonomy": { @@ -379,7 +465,7 @@ }, "kraken2_confidence": { "type": "number", - "default": 0, + "default": 0.0, "help_text": "Increasing the threshold will require more k-mers to match at a taxonomic levels and reduce the taxonomic levels shown until the threshold is met.", "description": "Confidence score threshold for taxonomic classification.", "minimum": 0, @@ -425,74 +511,9 @@ "asv_filtering": { "title": "ASV filtering", "type": "object", - "description": "", "default": "", + "fa_icon": "fas fa-filter", "properties": { - "vsearch_cluster": { - "type": "boolean", - "description": "Post-cluster ASVs with VSEARCH", - "help_text": "ASVs will be clustered with VSEARCH using the id value found in `--vsearch_cluster_id`." - }, - "vsearch_cluster_id": { - "type": "number", - "default": 0.97, - "minimum": 0.0, - "maximum": 1.0, - "description": "Pairwise Identity value used when post-clustering ASVs if `--vsearch_cluster` option is used (default: 0.97).", - "help_text": "Lowering or increasing this value can change the number ASVs left over after clustering." - }, - "filter_ssu": { - "type": "string", - "description": "Enable SSU filtering. Comma separated list of kingdoms (domains) in Barrnap, a combination (or one) of \"bac\", \"arc\", \"mito\", and \"euk\". ASVs that have their lowest evalue in that kingdoms are kept.", - "enum": [ - "bac,arc,mito,euk", - "bac", - "arc", - "mito", - "euk", - "bac,arc", - "bac,mito", - "bac,euk", - "arc,mito", - "arc,euk", - "mito,euk", - "bac,arc,mito", - "bac,mito,euk", - "arc,mito,euk" - ] - }, - "min_len_asv": { - "type": "integer", - "description": "Minimal ASV length", - "help_text": "Remove ASV that are below the minimum length threshold (default: filter is disabled, otherwise 1). Increasing the threshold might reduce false positive ASVs (e.g. PCR off-targets)." - }, - "max_len_asv": { - "type": "integer", - "description": "Maximum ASV length", - "help_text": "Remove ASV that are above the maximum length threshold (default: filter is disabled, otherwise 1000000). Lowering the threshold might reduce false positive ASVs (e.g. PCR off-targets)." - }, - "filter_codons": { - "type": "boolean", - "description": "Filter ASVs based on codon usage", - "help_text": "ASVs will be filtered to contain no stop codon in their coding sequence and that their length is a multiple of 3." - }, - "orf_start": { - "type": "integer", - "default": 1, - "description": "Starting position of codon tripletts", - "help_text": "By default, when `--filter_codons` is set, the codons start from the first position of the ASV sequences. The start of the codons can be changed to any position." - }, - "orf_end": { - "type": "integer", - "description": "Ending position of codon tripletts", - "help_text": "By default, when `--filter_codons` is set, the codons are checked until the end of the ASV sequences. If you would like to change this setting, you can specify until which position of the ASV sequences the codon triplets are checked.\n\nPlease note that the length of the ASV from the beginning or from the `--orf_start` until this position must be a multiple of 3." - }, - "stop_codons": { - "type": "string", - "default": "TAA,TAG", - "description": "Define stop codons", - "help_text": "By default, when `--filter_codons` is set, the codons `TAA,TAG` are set as stop codons. Here you can specify any comma-separated list of codons to be used as stop codons, e.g. `--stop_codons \"TAA,TAG,TGA\"`" - }, "exclude_taxa": { "type": "string", "default": "mitochondria,chloroplast", @@ -511,15 +532,14 @@ "description": "Prevalence filtering", "help_text": "Filtering low prevalent features from the feature table, e.g. keeping only features that are present in at least two samples can be achived by choosing a value of 2 (default: 1, meaning filter is disabled). Typically only used when having replicates for all samples.\n\nFor example to retain features that are present in at least two sample:\n\n```bash\n--min_samples 2\n```\n\nPlease note this is independent of abundance." } - }, - "fa_icon": "fas fa-filter" + } }, "downstream_analysis": { "title": "Downstream analysis", "type": "object", "description": "", "default": "", - "fa_icon": "fas fa-filter", + "fa_icon": "fas fa-bacteria", "properties": { "metadata_category": { "type": "string", @@ -600,10 +620,10 @@ }, "report_abstract": { "type": "string", - "default": null, "description": "Path to Markdown file (md) that replaces the 'Abstract' section" } - } + }, + "fa_icon": "fas fa-book-open" }, "skipping_specific_steps": { "title": "Skipping specific steps", @@ -671,7 +691,8 @@ "type": "boolean", "description": "Skip Markdown summary report" } - } + }, + "fa_icon": "fas fa-hand-paper" }, "generic_options": { "title": "Generic options", @@ -892,6 +913,9 @@ { "$ref": "#/definitions/amplicon_sequence_variants_asv_calculation" }, + { + "$ref": "#/definitions/asv_post_processing" + }, { "$ref": "#/definitions/taxonomic_database" }, From 83870b36e8abf4e210ff0d440650624dbbcb3635 Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 9 Nov 2023 15:46:59 +0100 Subject: [PATCH 12/17] report: small optimisations in wording --- assets/report_template.Rmd | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd index 6dff7817..294dde5d 100644 --- a/assets/report_template.Rmd +++ b/assets/report_template.Rmd @@ -370,7 +370,7 @@ cat(paste0(" Overall read quality profiles are displayed as heat map of the frequency of each quality score at each base position. The mean quality score at each position is shown by the green line, and the quartiles of the quality score distribution by the orange lines. The red line shows the scaled proportion of reads that extend to at least -that position. Original plots can be found [folder dada2/QC/](../dada2/QC/) with names that end in `_qual_stats.pdf`. +that position. Original plots can be found in folder [dada2/QC/](../dada2/QC/) with names that end in `_qual_stats.pdf`. ")) ``` @@ -426,8 +426,8 @@ cat(paste0(" Estimated error rates are displayed for each possible transition. The black line shows the estimated error rates after convergence of the machine-learning algorithm. The red line shows the error rates expected under the nominal definition of the Q-score. The estimated error rates (black line) should be a good fit to the observed rates -(points), and the error rates should drop with increased quality. Original plots can be found in -[folder dada2/QC/](../dada2/QC/) with names that end in `.err.pdf`. +(points), and the error rates should drop with increased quality. Original plots can be found in folder +[dada2/QC/](../dada2/QC/) with names that end in `.err.pdf`. ")) ``` @@ -1813,7 +1813,7 @@ if ( !isFALSE(params$dada2_ref_tax_title) ) { "- citation: `", params$dada2_ref_tax_citation, "`\n\n", sep = "") } else if (!isFALSE(params$dada2_taxonomy)) { cat("Taxonomic classification by DADA2:\n\n", - "- database: unknown - user provided\n\n", sep = "") + "- database: user provided file(s)\n\n", sep = "") } if ( !isFALSE(params$sintax_ref_tax_title) ) { @@ -1823,7 +1823,7 @@ if ( !isFALSE(params$sintax_ref_tax_title) ) { "- citation: `", params$sintax_ref_tax_citation, "`\n\n", sep = "") } else if (!isFALSE(params$sintax_taxonomy)) { cat("Taxonomic classification by SINTAX:\n\n", - "- database: unknown - user provided\n\n", sep = "") + "- database: user provided file\n\n", sep = "") } if ( !isFALSE(params$kraken2_ref_tax_title) ) { @@ -1833,7 +1833,7 @@ if ( !isFALSE(params$kraken2_ref_tax_title) ) { "- citation: `", params$kraken2_ref_tax_citation, "`\n\n", sep = "") } else if (!isFALSE(params$kraken2_taxonomy)) { cat("Taxonomic classification by Kraken2:\n\n", - "- database: unknown - user provided\n\n", sep = "") + "- database: user provided files\n\n", sep = "") } if ( !isFALSE(params$qiime2_ref_tax_title) ) { @@ -1843,7 +1843,7 @@ if ( !isFALSE(params$qiime2_ref_tax_title) ) { "- citation: `", params$qiime2_ref_tax_citation, "`\n\n", sep = "") } else if (!isFALSE(params$qiime2_taxonomy)) { cat("Taxonomic classification by QIIME2:\n\n", - "- database: unknown - user provided\n\n", sep = "") + "- database: user provided file\n\n", sep = "") } ``` From b8ab3494fbea524f7e942a19de69b7e7542e674d Mon Sep 17 00:00:00 2001 From: daniel Date: Thu, 9 Nov 2023 15:55:08 +0100 Subject: [PATCH 13/17] update CHANGELOG --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a8fc4eae..60f0403b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,10 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#657](https://github.com/nf-core/ampliseq/pull/657) - Improved parameter descriptions and sequence + ### `Fixed` - [#655](https://github.com/nf-core/ampliseq/pull/655) - Added `NUMBA_CACHE_DIR` to fix downstream analysis with QIIME2 that failed on some systems - [#656](https://github.com/nf-core/ampliseq/pull/656) - Moved conda-check to script-section and replaced `exit 1` with `error()` +- [#657](https://github.com/nf-core/ampliseq/pull/657) - Corrected inaccurate reporting of QIIME2 taxonomic classifications and ASV length filtering ### `Dependencies` From 76e3db7fa6fa5e310586d5a2baa3485f0c7e63fb Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Fri, 10 Nov 2023 09:11:19 +0100 Subject: [PATCH 14/17] Fix typo Co-authored-by: Till E. <64961761+tillenglert@users.noreply.github.com> --- assets/report_template.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd index 294dde5d..8c8fc21e 100644 --- a/assets/report_template.Rmd +++ b/assets/report_template.Rmd @@ -1001,7 +1001,7 @@ max_taxa <- lengths(regmatches(df$Taxon, gregexpr(";", df$Taxon)))+1 # Currently, all QIIME2 databases seem to have the same levels! But for compatibility, restrict number of levels to max_taxa level <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species") -level <- head(level, n= max(max_taxa) ) +level <- head(level, n = max(max_taxa) ) # Calculate the classified numbers/percent of asv n_asv_tax = nrow(asv_tax) From 2c5c0e95eb1f9f5735970ee9d7e46c5ce097cd44 Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 10 Nov 2023 15:32:22 +0100 Subject: [PATCH 15/17] bump version to 2.7.1 --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- tests/pipeline/doubleprimers.nf.test.snap | 2 +- tests/pipeline/fasta.nf.test.snap | 2 +- tests/pipeline/iontorrent.nf.test.snap | 2 +- tests/pipeline/multi.nf.test.snap | 2 +- tests/pipeline/novaseq.nf.test.snap | 2 +- tests/pipeline/pacbio_its.nf.test.snap | 2 +- tests/pipeline/pplace.nf.test.snap | 2 +- tests/pipeline/reftaxcustom.nf.test.snap | 2 +- tests/pipeline/single.nf.test.snap | 2 +- tests/pipeline/sintax.nf.test.snap | 2 +- tests/pipeline/test.nf.test.snap | 2 +- 14 files changed, 15 insertions(+), 15 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 60f0403b..cf0e5ce0 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). -## nf-core/ampliseq version 2.8.0dev +## nf-core/ampliseq version 2.7.1 - 2023-11-14 ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 64df13db..4fd6b6ea 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 5139e0ec..93e19e86 100644 --- a/nextflow.config +++ b/nextflow.config @@ -329,7 +329,7 @@ manifest { description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.8.0dev' + version = '2.7.1' doi = '10.5281/zenodo.1493841' } diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap index d7cc9dce..26ffdc7a 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=3.11.4, yaml=6.0}, 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}, 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=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, 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=2.7.1}}" ], "timestamp": "2023-07-27T13:49:03+0000" }, diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap index 6350712f..bde435d9 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "timestamp": "2023-05-28T21:06:17+0000" }, diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap index 420b3dd6..70bdf615 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "timestamp": "2023-06-20T01:42:35+0000" }, diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index 2c0382f0..10a5f78e 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=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.1}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap index 427cd40b..89bf199b 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "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 c211e2b6..0adfdad8 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{ASSIGNSH={pandas=1.1.5, python=3.9.1}, BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "timestamp": "2023-06-20T02:07:02+0000" }, diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index 4f64efa8..abd94f98 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap index 7dca4e3e..87538971 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=3.11.4, yaml=6.0}, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.1}}" ], "timestamp": "2023-05-28T21:18:54+0000" }, diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap index a31b986c..751d9a83 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "timestamp": "2023-05-28T20:35:33+0000" }, diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index 069c7fa8..aae3466c 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=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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}, QIIME2_INSEQ={qiime2=2023.7.0}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.1}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index 967f1369..8fc51fa0 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=3.11.4, yaml=6.0}, 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=2.8.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.4, yaml=6.0}, 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=2.7.1}}" ], "timestamp": "2023-05-28T20:55:32+0000" }, From b15b316a9ab531068b46391f9fb660ade7826ee5 Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 10 Nov 2023 15:36:23 +0100 Subject: [PATCH 16/17] update version in usage docs --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 74e2dcfc..38c2cc23 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -36,7 +36,7 @@ The typical command for running the pipeline is as follows: ```bash nextflow run nf-core/ampliseq \ - -r 2.7.0 \ + -r 2.7.1 \ -profile singularity \ --input "samplesheet.tsv" \ --FW_primer GTGYCAGCMGCCGCGGTAA \ @@ -45,7 +45,7 @@ nextflow run nf-core/ampliseq \ --outdir "./results" ``` -In this example, `--input` is the [Samplesheet input](#samplesheet-input), other options are [Direct FASTQ input](#direct-fastq-input) and [ASV/OTU fasta input](#asvotu-fasta-input). For more details on metadata, see [Metadata](#metadata). For [Reproducibility](#reproducibility), specify the version to run using `-r` (= release, e.g. 2.7.0, please use the most recent release). See the [nf-core/ampliseq website documentation](https://nf-co.re/ampliseq/parameters) for more information about pipeline specific parameters. +In this example, `--input` is the [Samplesheet input](#samplesheet-input), other options are [Direct FASTQ input](#direct-fastq-input) and [ASV/OTU fasta input](#asvotu-fasta-input). For more details on metadata, see [Metadata](#metadata). For [Reproducibility](#reproducibility), specify the version to run using `-r` (= release, e.g. 2.7.1, please use the most recent release). See the [nf-core/ampliseq website documentation](https://nf-co.re/ampliseq/parameters) for more information about pipeline specific parameters. It is possible to not provide primer sequences (`--FW_primer` & `--RV_primer`) and skip primer trimming using `--skip_cutadapt`, but this is only for data that indeed does not contain any PCR primers in their sequences. Also, metadata (`--metadata`) isnt required, but aids downstream analysis. From bb23cb01a8ea5309f966c49371c96d3be830f25b Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Mon, 13 Nov 2023 09:02:47 +0100 Subject: [PATCH 17/17] Update subworkflows/local/dada2_taxonomy_wf.nf Co-authored-by: Till E. <64961761+tillenglert@users.noreply.github.com> --- subworkflows/local/dada2_taxonomy_wf.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/dada2_taxonomy_wf.nf b/subworkflows/local/dada2_taxonomy_wf.nf index c0e5a85d..9aa64145 100644 --- a/subworkflows/local/dada2_taxonomy_wf.nf +++ b/subworkflows/local/dada2_taxonomy_wf.nf @@ -83,7 +83,7 @@ workflow DADA2_TAXONOMY_WF { //set file name prefix for SH assignments if (!params.skip_dada_addspecies) { ASV_SH_name = "ASV_tax_species_SH" - } else { + } else { ASV_SH_name = "ASV_tax_SH" } //find SHs