From bf66f46cfe1c5080b1019b1bee5961cac4261731 Mon Sep 17 00:00:00 2001 From: daniel Date: Mon, 16 Oct 2023 15:10:58 +0200 Subject: [PATCH 1/7] update nf-core modules --- modules.json | 10 ++--- .../custom/dumpsoftwareversions/main.nf | 6 +-- .../dumpsoftwareversions/tests/main.nf.test | 38 +++++++++++++++++++ .../tests/main.nf.test.snap | 27 +++++++++++++ modules/nf-core/fastqc/main.nf | 6 +-- modules/nf-core/fastqc/tests/main.nf.test | 23 +++++++---- .../nf-core/fastqc/tests/main.nf.test.snap | 10 +++++ modules/nf-core/mafft/main.nf | 6 +-- modules/nf-core/mafft/meta.yml | 1 + modules/nf-core/multiqc/main.nf | 6 +-- .../nf-core/fasta_newick_epang_gappa/meta.yml | 2 +- 11 files changed, 110 insertions(+), 25 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap diff --git a/modules.json b/modules.json index 85ebcba7..b85f77f5 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["modules"] }, "cutadapt": { @@ -27,7 +27,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", + "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0", "installed_by": ["modules"] }, "gappa/examineassign": { @@ -73,12 +73,12 @@ }, "mafft": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "feb29be775d9e41750180539e9a3bdce801d0609", "installed_by": ["fasta_newick_epang_gappa"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, "untar": { @@ -107,7 +107,7 @@ "nf-core": { "fasta_newick_epang_gappa": { "branch": "master", - "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653", + "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..eec1db10 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..8713b921 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + ], + "1": [ + "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + ], + "2": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + ], + "versions": [ + "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + ], + "yml": [ + "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + ] + } + ], + "timestamp": "2023-10-11T17:10:02.930699" + } +} diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..67209f79 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "bioconda::fastqc=0.12.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 3961de60..6437a144 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -1,13 +1,18 @@ nextflow_process { name "Test Process FASTQC" - script "modules/nf-core/fastqc/main.nf" + script "../main.nf" process "FASTQC" + tag "modules" + tag "modules_nfcore" tag "fastqc" test("Single-Read") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = [ @@ -21,12 +26,16 @@ nextflow_process { } then { - assert process.success - assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" - assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") - assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) } - } - } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..636a32ce --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index 420b6484..9b7d27c5 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -2,10 +2,10 @@ process MAFFT { tag "$meta.id" label 'process_high' - conda "bioconda::mafft=7.508" + conda "bioconda::mafft=7.520" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mafft:7.508--hec16e2b_0': - 'biocontainers/mafft:7.508--hec16e2b_0' }" + 'https://depot.galaxyproject.org/singularity/mafft:7.520--hec16e2b_1': + 'biocontainers/mafft:7.520--hec16e2b_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mafft/meta.yml b/modules/nf-core/mafft/meta.yml index a366a4b8..7cbf1087 100644 --- a/modules/nf-core/mafft/meta.yml +++ b/modules/nf-core/mafft/meta.yml @@ -1,6 +1,7 @@ name: mafft description: Multiple sequence alignment using MAFFT keywords: + - fasta - msa - multiple sequence alignment tools: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml b/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml index 2337aa58..60002c82 100644 --- a/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml +++ b/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml @@ -7,7 +7,7 @@ keywords: - alignment - fasta - newick -modules: +components: - hmmer/hmmbuild - hmmer/hmmalign - hmmer/eslalimask From 7ec4c155a91921dabf10f764e0de6b5ef13dbabd Mon Sep 17 00:00:00 2001 From: daniel Date: Mon, 16 Oct 2023 15:50:28 +0200 Subject: [PATCH 2/7] update DADA2 and PICRUSt2 --- modules/local/cutadapt_summary_merge.nf | 6 +++--- modules/local/dada2_addspecies.nf | 6 +++--- modules/local/dada2_denoising.nf | 6 +++--- modules/local/dada2_err.nf | 6 +++--- modules/local/dada2_filtntrim.nf | 6 +++--- modules/local/dada2_merge.nf | 1 + modules/local/dada2_quality.nf | 6 +++--- modules/local/dada2_rmchimera.nf | 6 +++--- modules/local/dada2_stats.nf | 6 +++--- modules/local/dada2_taxonomy.nf | 6 +++--- modules/local/format_pplacetax.nf | 6 +++--- modules/local/merge_stats.nf | 6 +++--- modules/local/metadata_all.nf | 6 +++--- modules/local/metadata_pairwise.nf | 6 +++--- modules/local/novaseq_err.nf | 6 +++--- modules/local/picrust.nf | 6 +++--- 16 files changed, 46 insertions(+), 45 deletions(-) diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf index 46b8ef2d..2b25fb42 100644 --- a/modules/local/cutadapt_summary_merge.nf +++ b/modules/local/cutadapt_summary_merge.nf @@ -2,10 +2,10 @@ process CUTADAPT_SUMMARY_MERGE { tag "${files}" label 'process_low' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: val(action) diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf index 4c83cca2..6f528264 100644 --- a/modules/local/dada2_addspecies.nf +++ b/modules/local/dada2_addspecies.nf @@ -3,10 +3,10 @@ process DADA2_ADDSPECIES { label 'process_high' label 'single_cpu' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: path(taxtable) diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf index 29d48186..ea07eadf 100644 --- a/modules/local/dada2_denoising.nf +++ b/modules/local/dada2_denoising.nf @@ -3,10 +3,10 @@ process DADA2_DENOISING { label 'process_medium' label 'process_long' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path("filtered/*"), path(errormodel) diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf index d4add8e8..cecca72f 100644 --- a/modules/local/dada2_err.nf +++ b/modules/local/dada2_err.nf @@ -2,10 +2,10 @@ process DADA2_ERR { tag "$meta.run" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf index 8ad6974c..9aca5912 100644 --- a/modules/local/dada2_filtntrim.nf +++ b/modules/local/dada2_filtntrim.nf @@ -2,10 +2,10 @@ process DADA2_FILTNTRIM { tag "$meta.id" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path(reads), val(trunclenf), val(trunclenr) diff --git a/modules/local/dada2_merge.nf b/modules/local/dada2_merge.nf index a910c6d4..8577dd4a 100644 --- a/modules/local/dada2_merge.nf +++ b/modules/local/dada2_merge.nf @@ -1,6 +1,7 @@ process DADA2_MERGE { label 'process_low' + // https://depot.galaxyproject.org/singularity/bioconductor-dada2=1.28.0--r43hf17093f_0 doesnt contain 'digest', so keep here v1.22.0 conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf index 3211fc6a..ff91c995 100644 --- a/modules/local/dada2_quality.nf +++ b/modules/local/dada2_quality.nf @@ -2,10 +2,10 @@ process DADA2_QUALITY { tag "$meta" label 'process_low' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf index b25973c9..0f25444f 100644 --- a/modules/local/dada2_rmchimera.nf +++ b/modules/local/dada2_rmchimera.nf @@ -2,10 +2,10 @@ process DADA2_RMCHIMERA { tag "$meta.run" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path(seqtab) diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf index f829a99a..2fe792e5 100644 --- a/modules/local/dada2_stats.nf +++ b/modules/local/dada2_stats.nf @@ -2,10 +2,10 @@ process DADA2_STATS { tag "$meta.run" label 'process_low' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path("filter_and_trim_files/*"), path(denoised), path(mergers), path(seqtab_nochim) diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf index b7919185..4be292d2 100644 --- a/modules/local/dada2_taxonomy.nf +++ b/modules/local/dada2_taxonomy.nf @@ -2,10 +2,10 @@ process DADA2_TAXONOMY { tag "${fasta},${database}" label 'process_high' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: path(fasta) diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf index d159627c..1861a365 100644 --- a/modules/local/format_pplacetax.nf +++ b/modules/local/format_pplacetax.nf @@ -2,10 +2,10 @@ process FORMAT_PPLACETAX { tag "${tax.baseName}" label 'process_high' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path(tax) diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf index 55b2cf83..b2e2cb8c 100644 --- a/modules/local/merge_stats.nf +++ b/modules/local/merge_stats.nf @@ -1,10 +1,10 @@ process MERGE_STATS { label 'process_low' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: path('file1.tsv') diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf index 67d148e9..8993d1ca 100644 --- a/modules/local/metadata_all.nf +++ b/modules/local/metadata_all.nf @@ -2,10 +2,10 @@ process METADATA_ALL { tag "$metadata" label 'process_low' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: path(metadata) diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf index cfa16a8c..6dd9ab11 100644 --- a/modules/local/metadata_pairwise.nf +++ b/modules/local/metadata_pairwise.nf @@ -2,10 +2,10 @@ process METADATA_PAIRWISE { tag "$metadata" label 'process_low' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: path(metadata) diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf index 4a9fbe8e..991fa803 100644 --- a/modules/local/novaseq_err.nf +++ b/modules/local/novaseq_err.nf @@ -2,10 +2,10 @@ process NOVASEQ_ERR { tag "$meta.run" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" + conda "bioconda::bioconductor-dada2=1.28.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" input: tuple val(meta), path(errormodel) diff --git a/modules/local/picrust.nf b/modules/local/picrust.nf index 0a0d6d2d..0f09a899 100644 --- a/modules/local/picrust.nf +++ b/modules/local/picrust.nf @@ -2,10 +2,10 @@ process PICRUST { tag "${seq},${abund}" label 'process_medium' - conda "bioconda::picrust2=2.5.0" + conda "bioconda::picrust2=2.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picrust2:2.5.0--pyhdfd78af_0' : - 'biocontainers/picrust2:2.5.0--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picrust2:2.5.2--pyhdfd78af_0' : + 'biocontainers/picrust2:2.5.2--pyhdfd78af_0' }" input: path(seq) From 574888616d1f023d680ec3358f55686609089347 Mon Sep 17 00:00:00 2001 From: daniel Date: Mon, 16 Oct 2023 15:56:59 +0200 Subject: [PATCH 3/7] update test.snap --- 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 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap index 10544679..a20349f9 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-07-27T13:49:03+0000" }, diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap index 77900c61..66e2041b 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=3.11.0, yaml=6.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:06:17+0000" }, diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap index c7fbfb89..3d3ab087 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" ], "timestamp": "2023-06-20T01:42:35+0000" }, diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index 25b1437c..03899270 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=3.11.0, yaml=6.0}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, QIIME2_INSEQ={qiime2=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap index 737b16a2..85eefe21 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=3.11.0, yaml=6.0}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, 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=2.7.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" ], "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 775e5195..06d4a727 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, 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=2.7.0dev}}" + "{ASSIGNSH={pandas=1.1.5, python=3.9.1}, BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" ], "timestamp": "2023-06-20T02:07:02+0000" }, diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index 9ee79d29..b5e36b14 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap index 2a91fce2..eda25b73 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:18:54+0000" }, diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap index ad74ef74..b9db1804 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, PHYLOSEQ={R=4.3.0, phyloseq=1.44.0}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:35:33+0000" }, diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index 5f360a4b..87bb4ed1 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index 1334d01e..c842bdc5 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, 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=2022.11.1}, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2022.11.1}, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:55:32+0000" }, From 7701a807d4b1a11a56f61dc4b003ea3418f51bdf Mon Sep 17 00:00:00 2001 From: daniel Date: Mon, 16 Oct 2023 16:02:42 +0200 Subject: [PATCH 4/7] update CHANGELOG --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fff410e2..fd5c4652 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` +- [#646](https://github.com/nf-core/ampliseq/pull/646) - Updated dependencies, see below: + +| software | previously | now | +| -------- | ---------- | ------ | +| FASTQC | 0.11.9 | 0.12.1 | +| DADA2 | 1.22.0 | 1.28.0 | +| PICRUSt2 | 2.5.0 | 2.5.2 | + ### `Removed` ## nf-core/ampliseq version 2.6.1 - 2023-06-28 From a2b3aaff98c1e3fe30313e24b91c28687acadf68 Mon Sep 17 00:00:00 2001 From: daniel Date: Mon, 16 Oct 2023 16:21:17 +0200 Subject: [PATCH 5/7] update QIIME2 --- CHANGELOG.md | 1 + conf/ref_databases.config | 6 +++--- 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_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 | 2 +- modules/local/qiime2_tree.nf | 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 +- 36 files changed, 38 insertions(+), 37 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fd5c4652..43059552 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | FASTQC | 0.11.9 | 0.12.1 | | DADA2 | 1.22.0 | 1.28.0 | | PICRUSt2 | 2.5.0 | 2.5.2 | +| QIIME2 | 2022.11 | 2023.7 | ### `Removed` diff --git a/conf/ref_databases.config b/conf/ref_databases.config index 43e1eb81..1f50df7d 100644 --- a/conf/ref_databases.config +++ b/conf/ref_databases.config @@ -245,14 +245,14 @@ params { //SILVA for QIIME2 v2021.2, see https://docs.qiime2.org/2021.2/data-resources/#silva-16s-18s-rrna 'silva=138' { title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138" - file = [ "https://data.qiime2.org/2022.11/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2022.11/common/silva-138-99-tax.qza" ] + file = [ "https://data.qiime2.org/2023.7/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2023.7/common/silva-138-99-tax.qza" ] citation = "https://www.arb-silva.de/; Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931" license = "https://www.arb-silva.de/silva-license-information/" fmtscript = "taxref_reformat_qiime_silva138.sh" } 'silva' { title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138" - file = [ "https://data.qiime2.org/2022.11/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2022.11/common/silva-138-99-tax.qza" ] + file = [ "https://data.qiime2.org/2023.7/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2023.7/common/silva-138-99-tax.qza" ] citation = "https://www.arb-silva.de/; Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931" license = "https://www.arb-silva.de/silva-license-information/" fmtscript = "taxref_reformat_qiime_silva138.sh" @@ -302,7 +302,7 @@ params { } 'greengenes85' { title = "Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only" - file = [ "https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otus.fasta", "https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otu_taxonomy.txt" ] + file = [ "https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otus.fasta", "https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otu_taxonomy.txt" ] citation = "McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139" fmtscript = "taxref_reformat_qiime_greengenes85.sh" } diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index 9ff9c782..273749ba 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -1,7 +1,7 @@ process QIIME2_ALPHARAREFACTION { label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 165ca45f..52c599c4 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -5,7 +5,7 @@ process QIIME2_ANCOM_ASV { label 'process_long' label 'error_ignore' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index 717e7286..3c065bb3 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -3,7 +3,7 @@ process QIIME2_ANCOM_TAX { label 'process_medium' label 'single_cpu' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index bb0c8aeb..a06100d4 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -1,7 +1,7 @@ process QIIME2_BARPLOT { label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index c32fff03..96910c9a 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -2,7 +2,7 @@ process QIIME2_CLASSIFY { tag "${repseq},${trained_classifier}" label 'process_high' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 78b15dd3..6b81f00e 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ADONIS { tag "${core.baseName} - ${formula}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index ae1db546..baebc03e 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ALPHA { tag "${core.baseName}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 8f73ff2c..44df25f9 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETA { tag "${core.baseName} - ${category}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index aba4afa8..b29bd99e 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETAORD { tag "${core.baseName}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index ad9a5cd8..22235dfb 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -1,7 +1,7 @@ process QIIME2_DIVERSITY_CORE { label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 9bfe0d0a..57c03a5e 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -1,7 +1,7 @@ process QIIME2_EXPORT_ABSOLUTE { label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 9ed1b322..58e05b58 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -1,7 +1,7 @@ process QIIME2_EXPORT_RELASV { label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index ea2cf21a..c5b93d7c 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -1,7 +1,7 @@ process QIIME2_EXPORT_RELTAX { label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 3a10c107..6889befb 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -3,7 +3,7 @@ process QIIME2_EXTRACT { label 'process_low' label 'single_cpu' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index 44bcfaae..d47ee14f 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -2,7 +2,7 @@ process QIIME2_FEATURETABLE_GROUP { tag "${category}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 4bdd7e39..7f64e7e2 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -2,7 +2,7 @@ process QIIME2_FILTERSAMPLES { tag "${filter}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 1f26ab10..39cbb82c 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -2,7 +2,7 @@ process QIIME2_FILTERTAXA { tag "taxa:${exclude_taxa};min-freq:${min_frequency};min-samples:${min_samples}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index aea70bb7..d4848ba7 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -2,7 +2,7 @@ process QIIME2_INASV { tag "${asv}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 0cc3aca8..7c7c2007 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -2,7 +2,7 @@ process QIIME2_INSEQ { tag "${seq}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index 50c24da8..b9c3b039 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -2,7 +2,7 @@ process QIIME2_INTAX { tag "${tax}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index 620e74c0..a7a3ff3b 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -2,7 +2,7 @@ process QIIME2_INTREE { tag "${meta.id}:${meta.model}" label 'process_low' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 289fd6a6..4c4d69b2 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -3,7 +3,7 @@ process QIIME2_TRAIN { label 'process_high' label 'single_cpu' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index c870842f..6e7a89fe 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -1,7 +1,7 @@ process QIIME2_TREE { label 'process_medium' - container "qiime2/core:2022.11" + container "qiime2/core:2023.7" // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap index a20349f9..2f02b71a 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-07-27T13:49:03+0000" }, diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap index 66e2041b..d8aca29a 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=3.11.0, yaml=6.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:06:17+0000" }, diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap index 3d3ab087..9f06e7e9 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" ], "timestamp": "2023-06-20T01:42:35+0000" }, diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index 03899270..7495830b 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=3.11.0, yaml=6.0}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap index 85eefe21..c943d632 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=3.11.0, yaml=6.0}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" ], "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 06d4a727..e6498000 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" + "{ASSIGNSH={pandas=1.1.5, python=3.9.1}, BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" ], "timestamp": "2023-06-20T02:07:02+0000" }, diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index b5e36b14..f0388a56 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap index eda25b73..8fa64d9e 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:18:54+0000" }, diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap index b9db1804..403bc397 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:35:33+0000" }, diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index 87bb4ed1..a989e506 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, 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=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index c842bdc5..4e53e50d 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=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.28.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.28.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.28.0}, DADA2_TAXONOMY={R=4.1.1, 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=2022.11.1}, 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=2.7.0dev}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:55:32+0000" }, From 9e2a61e1912ff074ab39d185c015da14ab3b8b53 Mon Sep 17 00:00:00 2001 From: daniel Date: Mon, 16 Oct 2023 16:39:52 +0200 Subject: [PATCH 6/7] update test.snap --- conf/ref_databases.config | 2 +- tests/pipeline/doubleprimers.nf.test.snap | 2 +- tests/pipeline/fasta.nf.test.snap | 2 +- tests/pipeline/iontorrent.nf.test.snap | 6 +++--- tests/pipeline/multi.nf.test.snap | 4 ++-- tests/pipeline/novaseq.nf.test.snap | 6 +++--- tests/pipeline/pacbio_its.nf.test.snap | 6 +++--- tests/pipeline/pplace.nf.test.snap | 2 +- tests/pipeline/reftaxcustom.nf.test.snap | 4 ++-- tests/pipeline/single.nf.test.snap | 4 ++-- tests/pipeline/sintax.nf.test.snap | 4 ++-- tests/pipeline/test.nf.test.snap | 4 ++-- 12 files changed, 23 insertions(+), 23 deletions(-) diff --git a/conf/ref_databases.config b/conf/ref_databases.config index 1f50df7d..c80820ec 100644 --- a/conf/ref_databases.config +++ b/conf/ref_databases.config @@ -242,7 +242,7 @@ params { } //QIIME2 taxonomic reference databases qiime_ref_databases { - //SILVA for QIIME2 v2021.2, see https://docs.qiime2.org/2021.2/data-resources/#silva-16s-18s-rrna + //SILVA for QIIME2 v2023.7, see https://docs.qiime2.org/2023.7/data-resources/#silva-16s-18s-rrna 'silva=138' { title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138" file = [ "https://data.qiime2.org/2023.7/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2023.7/common/silva-138-99-tax.qza" ] diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap index 2f02b71a..e3efb4bd 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-07-27T13:49:03+0000" }, diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap index d8aca29a..028b6215 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=3.11.0, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:06:17+0000" }, diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap index 9f06e7e9..2ae40934 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-06-20T01:42:35+0000" }, @@ -45,8 +45,8 @@ }, "multiqc": { "content": [ - "multiqc_fastqc.txt:md5,a64a5b74f7f336909d706a5747ad596d", - "multiqc_general_stats.txt:md5,e50f532aa2a52a79a2f76b66f970771c", + "multiqc_fastqc.txt:md5,6f1a5196d0840a35166b88e5b52bfcdd", + "multiqc_general_stats.txt:md5,8b11410948277038a1ba1a77bb30557f", "multiqc_cutadapt.txt:md5,9315dca2bd7b5476e54a9ccd8b1f24d5" ], "timestamp": "2023-06-20T01:42:35+0000" diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index 7495830b..3c23ce71 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=3.11.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, @@ -47,7 +47,7 @@ "multiqc": { "content": [ "multiqc_general_stats.txt:md5,5692ee73c6933866807706d29b15c880", - "multiqc_fastqc.txt:md5,3a4417c7d95a9bbe17751dc974157cd3" + "multiqc_fastqc.txt:md5,147764e40079c3abf97a17cfe2275c52" ], "timestamp": "2023-05-28T21:15:03+0000" } diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap index c943d632..7124f059 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-06-20T00:10:02+0000" }, @@ -23,8 +23,8 @@ }, "multiqc": { "content": [ - "multiqc_fastqc.txt:md5,ac8744f9d5d4dc51957a719183074c2f", - "multiqc_general_stats.txt:md5,c4d6a79d9c271a72c2f6a7ef66fe39c6" + "multiqc_fastqc.txt:md5,a99548124efd185a7d4e33245edcb81b", + "multiqc_general_stats.txt:md5,195ce3e0c1b032459040613802d25d50" ], "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 e6498000..0bb2b52c 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-06-20T02:07:02+0000" }, @@ -67,8 +67,8 @@ }, "multiqc": { "content": [ - "multiqc_fastqc.txt:md5,d289cd1a2523f9ad66e93a895dcbe52c", - "multiqc_general_stats.txt:md5,05682be32bc30bc4610f0ca608cafe67", + "multiqc_fastqc.txt:md5,e646906d896ac4514235ae263566a1a8", + "multiqc_general_stats.txt:md5,07a1affcf11214b293ea804eb560a2fb", "multiqc_cutadapt.txt:md5,1b3b6833e78db31ab12e5c16b7fa1d73" ], "timestamp": "2023-06-20T02:07:02+0000" diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index f0388a56..8bcc4675 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap index 8fa64d9e..8c536c4c 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:18:54+0000" }, @@ -52,7 +52,7 @@ }, "multiqc": { "content": [ - "multiqc_fastqc.txt:md5,3a4417c7d95a9bbe17751dc974157cd3", + "multiqc_fastqc.txt:md5,147764e40079c3abf97a17cfe2275c52", "multiqc_general_stats.txt:md5,88c2b9e6d02b83afe4f9551e6c9a91a7", "multiqc_cutadapt.txt:md5,330a7b72dc671ca99fcb3fb84b6776c1" ], diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap index 403bc397..fae2e4ae 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:35:33+0000" }, @@ -45,7 +45,7 @@ }, "multiqc": { "content": [ - "multiqc_fastqc.txt:md5,16ff42a422cd6c6a787c97febe12aa69", + "multiqc_fastqc.txt:md5,ede83a16cac9730e6b961ed051c1de0e", "multiqc_general_stats.txt:md5,d22c32eed33d046503751b23670db5e4", "multiqc_cutadapt.txt:md5,4311a83074d94040405937e02773c5a9" ], diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index a989e506..ce08db9d 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, @@ -60,7 +60,7 @@ }, "multiqc": { "content": [ - "multiqc_general_stats.txt:md5,05682be32bc30bc4610f0ca608cafe67", + "multiqc_general_stats.txt:md5,07a1affcf11214b293ea804eb560a2fb", "multiqc_cutadapt.txt:md5,1b3b6833e78db31ab12e5c16b7fa1d73" ], "timestamp": "2023-06-20T16:40:18+0000" diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index 4e53e50d..cc842963 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=3.11.0, 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=4.1.1, ShortRead=1.52.0, 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}, 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=2.7.0dev}}" + "{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}, 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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:55:32+0000" }, @@ -57,7 +57,7 @@ }, "multiqc": { "content": [ - "multiqc_fastqc.txt:md5,3a4417c7d95a9bbe17751dc974157cd3", + "multiqc_fastqc.txt:md5,147764e40079c3abf97a17cfe2275c52", "multiqc_general_stats.txt:md5,88c2b9e6d02b83afe4f9551e6c9a91a7", "multiqc_cutadapt.txt:md5,330a7b72dc671ca99fcb3fb84b6776c1" ], From 5c8c7c4beb424bbaab103fa163faabc1e7f90150 Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 17 Oct 2023 08:14:36 +0200 Subject: [PATCH 7/7] update test.snap again --- tests/pipeline/doubleprimers.nf.test.snap | 2 +- tests/pipeline/multi.nf.test.snap | 2 +- tests/pipeline/pplace.nf.test.snap | 2 +- tests/pipeline/sintax.nf.test.snap | 2 +- tests/pipeline/test.nf.test.snap | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/pipeline/doubleprimers.nf.test.snap b/tests/pipeline/doubleprimers.nf.test.snap index e3efb4bd..d6225d67 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-07-27T13:49:03+0000" }, diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index 3c23ce71..95e2fbf0 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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index 8bcc4675..ccc507d5 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index ce08db9d..27130565 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}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_SINTAX={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index cc842963..d3b27f80 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}, 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=2.7.0dev}}" + "{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=2.7.0dev}}" ], "timestamp": "2023-05-28T20:55:32+0000" },