From b06e117ae9e5148ddab35796101d4d96cefd1014 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:01:01 +0200 Subject: [PATCH 1/9] remove cleanup true for test full --- conf/test_full.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 16d15108..a17d4fa8 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' From 682fa04d342adbec523d1ac64fc87f6a0d3fbed0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:08:25 +0200 Subject: [PATCH 2/9] quay.io image instead of the docker.io one --- modules/local/format_fastainput.nf | 2 +- modules/local/rename_raw_data_files.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/format_fastainput.nf b/modules/local/format_fastainput.nf index 92cb587b..5f261800 100644 --- a/modules/local/format_fastainput.nf +++ b/modules/local/format_fastainput.nf @@ -4,7 +4,7 @@ process FORMAT_FASTAINPUT { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'docker.io/ubuntu:20.04' }" + 'nf-core/ubuntu:20.04' }" input: path(fastain) diff --git a/modules/local/rename_raw_data_files.nf b/modules/local/rename_raw_data_files.nf index 8f8016bb..52376e37 100644 --- a/modules/local/rename_raw_data_files.nf +++ b/modules/local/rename_raw_data_files.nf @@ -5,7 +5,7 @@ process RENAME_RAW_DATA_FILES { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'docker.io/ubuntu:20.04' }" + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(reads) From 2ccbf1e83fcaea0781f0d6410050960adc3e4e11 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:09:07 +0200 Subject: [PATCH 3/9] no need for quay.io as it's a default registry --- modules/local/assignsh.nf | 2 +- modules/local/barrnap.nf | 2 +- modules/local/barrnapsummary.nf | 2 +- modules/local/combine_table.nf | 2 +- modules/local/cutadapt_summary_merge.nf | 2 +- modules/local/dada2_addspecies.nf | 2 +- modules/local/dada2_denoising.nf | 2 +- modules/local/dada2_err.nf | 2 +- modules/local/dada2_filtntrim.nf | 2 +- modules/local/dada2_merge.nf | 2 +- modules/local/dada2_quality.nf | 2 +- modules/local/dada2_rmchimera.nf | 2 +- modules/local/dada2_stats.nf | 2 +- modules/local/dada2_taxonomy.nf | 2 +- modules/local/filter_codons.nf | 2 +- modules/local/filter_len_asv.nf | 2 +- modules/local/filter_ssu.nf | 2 +- modules/local/filter_stats.nf | 2 +- modules/local/format_pplacetax.nf | 2 +- modules/local/format_taxresults.nf | 2 +- modules/local/format_taxresults_sintax.nf | 2 +- modules/local/itsx_cutasv.nf | 2 +- modules/local/merge_stats.nf | 2 +- modules/local/metadata_all.nf | 2 +- modules/local/metadata_pairwise.nf | 2 +- modules/local/novaseq_err.nf | 3 ++- modules/local/picrust.nf | 2 +- modules/local/sbdiexport.nf | 2 +- modules/local/sbdiexportreannotate.nf | 2 +- modules/local/trunclen.nf | 2 +- 30 files changed, 31 insertions(+), 30 deletions(-) diff --git a/modules/local/assignsh.nf b/modules/local/assignsh.nf index 72dceb39..521ed6f2 100644 --- a/modules/local/assignsh.nf +++ b/modules/local/assignsh.nf @@ -5,7 +5,7 @@ process ASSIGNSH { conda "conda-forge::pandas=1.1.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.1.5': - 'quay.io/biocontainers/pandas:1.1.5' }" + 'biocontainers/pandas:1.1.5' }" input: path asvtable diff --git a/modules/local/barrnap.nf b/modules/local/barrnap.nf index 0341e6e8..1877d000 100644 --- a/modules/local/barrnap.nf +++ b/modules/local/barrnap.nf @@ -5,7 +5,7 @@ process BARRNAP { conda "bioconda::barrnap=0.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/barrnap:0.9--hdfd78af_4' : - 'quay.io/biocontainers/barrnap:0.9--hdfd78af_4' }" + 'biocontainers/barrnap:0.9--hdfd78af_4' }" input: path(fasta) diff --git a/modules/local/barrnapsummary.nf b/modules/local/barrnapsummary.nf index 7d6ecbb8..20064bcb 100644 --- a/modules/local/barrnapsummary.nf +++ b/modules/local/barrnapsummary.nf @@ -4,7 +4,7 @@ process BARRNAPSUMMARY { conda "conda-forge::python=3.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9' : - 'quay.io/biocontainers/python:3.9' }" + 'biocontainers/python:3.9' }" input: path predictions diff --git a/modules/local/combine_table.nf b/modules/local/combine_table.nf index 6fdd9962..bfde2ab5 100644 --- a/modules/local/combine_table.nf +++ b/modules/local/combine_table.nf @@ -4,7 +4,7 @@ process COMBINE_TABLE { conda "bioconda::bioconductor-biostrings=2.58.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' : - 'quay.io/biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }" + 'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }" input: path(table) diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf index 1df4bc3d..46b8ef2d 100644 --- a/modules/local/cutadapt_summary_merge.nf +++ b/modules/local/cutadapt_summary_merge.nf @@ -5,7 +5,7 @@ process CUTADAPT_SUMMARY_MERGE { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: val(action) diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf index a002148b..4c83cca2 100644 --- a/modules/local/dada2_addspecies.nf +++ b/modules/local/dada2_addspecies.nf @@ -6,7 +6,7 @@ process DADA2_ADDSPECIES { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: path(taxtable) diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf index 5e94c335..29d48186 100644 --- a/modules/local/dada2_denoising.nf +++ b/modules/local/dada2_denoising.nf @@ -6,7 +6,7 @@ process DADA2_DENOISING { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path("filtered/*"), path(errormodel) diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf index 790bc159..d4add8e8 100644 --- a/modules/local/dada2_err.nf +++ b/modules/local/dada2_err.nf @@ -5,7 +5,7 @@ process DADA2_ERR { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf index 26982a51..1a38189f 100644 --- a/modules/local/dada2_filtntrim.nf +++ b/modules/local/dada2_filtntrim.nf @@ -5,7 +5,7 @@ process DADA2_FILTNTRIM { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path(reads), val(trunclenf), val(trunclenr) diff --git a/modules/local/dada2_merge.nf b/modules/local/dada2_merge.nf index edf5a47a..a910c6d4 100644 --- a/modules/local/dada2_merge.nf +++ b/modules/local/dada2_merge.nf @@ -4,7 +4,7 @@ process DADA2_MERGE { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: path(files) diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf index 4e64772d..3211fc6a 100644 --- a/modules/local/dada2_quality.nf +++ b/modules/local/dada2_quality.nf @@ -5,7 +5,7 @@ process DADA2_QUALITY { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf index f3fa542e..b25973c9 100644 --- a/modules/local/dada2_rmchimera.nf +++ b/modules/local/dada2_rmchimera.nf @@ -5,7 +5,7 @@ process DADA2_RMCHIMERA { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path(seqtab) diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf index 81e0f4da..f829a99a 100644 --- a/modules/local/dada2_stats.nf +++ b/modules/local/dada2_stats.nf @@ -5,7 +5,7 @@ process DADA2_STATS { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path("filter_and_trim_files/*"), path(denoised), path(mergers), path(seqtab_nochim) diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf index c9a65381..b7919185 100644 --- a/modules/local/dada2_taxonomy.nf +++ b/modules/local/dada2_taxonomy.nf @@ -5,7 +5,7 @@ process DADA2_TAXONOMY { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: path(fasta) diff --git a/modules/local/filter_codons.nf b/modules/local/filter_codons.nf index a3b51d2d..972f5e94 100644 --- a/modules/local/filter_codons.nf +++ b/modules/local/filter_codons.nf @@ -5,7 +5,7 @@ process FILTER_CODONS { conda "conda-forge::pandas=1.1.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.1.5': - 'quay.io/biocontainers/pandas:1.1.5' }" + 'biocontainers/pandas:1.1.5' }" input: path(fasta) diff --git a/modules/local/filter_len_asv.nf b/modules/local/filter_len_asv.nf index c7fc41d2..8e9306f1 100644 --- a/modules/local/filter_len_asv.nf +++ b/modules/local/filter_len_asv.nf @@ -5,7 +5,7 @@ process FILTER_LEN_ASV { conda "bioconda::bioconductor-biostrings=2.58.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' : - 'quay.io/biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }" + 'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }" input: path(fasta) diff --git a/modules/local/filter_ssu.nf b/modules/local/filter_ssu.nf index 21b04705..ac423f45 100644 --- a/modules/local/filter_ssu.nf +++ b/modules/local/filter_ssu.nf @@ -5,7 +5,7 @@ process FILTER_SSU { conda "bioconductor::biostrings=2.58.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' : - 'quay.io/biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }" + 'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }" input: path(fasta) diff --git a/modules/local/filter_stats.nf b/modules/local/filter_stats.nf index 55a737c9..d83e48f4 100644 --- a/modules/local/filter_stats.nf +++ b/modules/local/filter_stats.nf @@ -4,7 +4,7 @@ process FILTER_STATS { conda "conda-forge::pandas=1.1.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.1.5' : - 'quay.io/biocontainers/pandas:1.1.5' }" + 'biocontainers/pandas:1.1.5' }" input: path(unfiltered) diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf index 09376354..d159627c 100644 --- a/modules/local/format_pplacetax.nf +++ b/modules/local/format_pplacetax.nf @@ -5,7 +5,7 @@ process FORMAT_PPLACETAX { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: tuple val(meta), path(tax) diff --git a/modules/local/format_taxresults.nf b/modules/local/format_taxresults.nf index ebe0115d..5e7cc7c9 100644 --- a/modules/local/format_taxresults.nf +++ b/modules/local/format_taxresults.nf @@ -4,7 +4,7 @@ process FORMAT_TAXRESULTS { conda "conda-forge::pandas=1.1.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.1.5' : - 'quay.io/biocontainers/pandas:1.1.5' }" + 'biocontainers/pandas:1.1.5' }" input: path(taxtable) diff --git a/modules/local/format_taxresults_sintax.nf b/modules/local/format_taxresults_sintax.nf index 2496a7b3..eaf74a15 100644 --- a/modules/local/format_taxresults_sintax.nf +++ b/modules/local/format_taxresults_sintax.nf @@ -4,7 +4,7 @@ process FORMAT_TAXRESULTS_SINTAX { conda "conda-forge::python=3.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9' : - 'quay.io/biocontainers/python:3.9' }" + 'biocontainers/python:3.9' }" input: tuple val(meta), path(taxtable) diff --git a/modules/local/itsx_cutasv.nf b/modules/local/itsx_cutasv.nf index cb863be9..e5813816 100644 --- a/modules/local/itsx_cutasv.nf +++ b/modules/local/itsx_cutasv.nf @@ -4,7 +4,7 @@ process ITSX_CUTASV { conda "bioconda::itsx=1.1.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/itsx:1.1.3--hdfd78af_1' : - 'quay.io/biocontainers/itsx:1.1.3--hdfd78af_1' }" + 'biocontainers/itsx:1.1.3--hdfd78af_1' }" input: path fasta diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf index d15ab7b3..55b2cf83 100644 --- a/modules/local/merge_stats.nf +++ b/modules/local/merge_stats.nf @@ -4,7 +4,7 @@ process MERGE_STATS { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: path('file1.tsv') diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf index 8570e6b1..67d148e9 100644 --- a/modules/local/metadata_all.nf +++ b/modules/local/metadata_all.nf @@ -5,7 +5,7 @@ process METADATA_ALL { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: path(metadata) diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf index cce98e51..cfa16a8c 100644 --- a/modules/local/metadata_pairwise.nf +++ b/modules/local/metadata_pairwise.nf @@ -5,7 +5,7 @@ process METADATA_PAIRWISE { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" input: path(metadata) diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf index 2db53cbc..4a9fbe8e 100644 --- a/modules/local/novaseq_err.nf +++ b/modules/local/novaseq_err.nf @@ -5,7 +5,8 @@ process NOVASEQ_ERR { conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' : - 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + 'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }" + input: tuple val(meta), path(errormodel) diff --git a/modules/local/picrust.nf b/modules/local/picrust.nf index 16192665..0a0d6d2d 100644 --- a/modules/local/picrust.nf +++ b/modules/local/picrust.nf @@ -5,7 +5,7 @@ process PICRUST { conda "bioconda::picrust2=2.5.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picrust2:2.5.0--pyhdfd78af_0' : - 'quay.io/biocontainers/picrust2:2.5.0--pyhdfd78af_0' }" + 'biocontainers/picrust2:2.5.0--pyhdfd78af_0' }" input: path(seq) diff --git a/modules/local/sbdiexport.nf b/modules/local/sbdiexport.nf index c2c347cb..ce469338 100644 --- a/modules/local/sbdiexport.nf +++ b/modules/local/sbdiexport.nf @@ -5,7 +5,7 @@ process SBDIEXPORT { conda "conda-forge::r-tidyverse=1.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-tidyverse:1.2.1' : - 'quay.io/biocontainers/r-tidyverse:1.2.1' }" + 'biocontainers/r-tidyverse:1.2.1' }" input: path asvtable diff --git a/modules/local/sbdiexportreannotate.nf b/modules/local/sbdiexportreannotate.nf index 50125217..f06fae36 100644 --- a/modules/local/sbdiexportreannotate.nf +++ b/modules/local/sbdiexportreannotate.nf @@ -5,7 +5,7 @@ process SBDIEXPORTREANNOTATE { conda "conda-forge::r-tidyverse=1.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-tidyverse:1.2.1' : - 'quay.io/biocontainers/r-tidyverse:1.2.1' }" + 'biocontainers/r-tidyverse:1.2.1' }" input: path taxonomytable diff --git a/modules/local/trunclen.nf b/modules/local/trunclen.nf index faea5bf0..abfa4e6b 100644 --- a/modules/local/trunclen.nf +++ b/modules/local/trunclen.nf @@ -5,7 +5,7 @@ process TRUNCLEN { conda "conda-forge::pandas=1.1.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.1.5' : - 'quay.io/biocontainers/pandas:1.1.5' }" + 'biocontainers/pandas:1.1.5' }" input: tuple val(meta), path(qual_stats) From 8a31bbd042f2e5029eddd7d3094c2303a1045354 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:16:38 +0200 Subject: [PATCH 4/9] update nf-core/modules --- modules.json | 34 +++++++++---------- .../custom/dumpsoftwareversions/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 3 +- modules/nf-core/cutadapt/main.nf | 15 +++++++- modules/nf-core/cutadapt/meta.yml | 2 +- modules/nf-core/epang/place/main.nf | 2 +- modules/nf-core/epang/split/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/gappa/examineassign/main.nf | 2 +- modules/nf-core/gappa/examinegraft/main.nf | 2 +- modules/nf-core/gappa/examineheattree/main.nf | 2 +- modules/nf-core/hmmer/eslalimask/main.nf | 2 +- modules/nf-core/hmmer/eslreformat/main.nf | 2 +- modules/nf-core/hmmer/hmmalign/main.nf | 2 +- modules/nf-core/hmmer/hmmbuild/main.nf | 2 +- modules/nf-core/mafft/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 2 +- modules/nf-core/vsearch/sintax/main.nf | 2 +- modules/nf-core/vsearch/usearchglobal/main.nf | 2 +- .../nf-core/vsearch/usearchglobal/meta.yml | 4 +-- .../nf-core/fasta_newick_epang_gappa/meta.yml | 25 +++++++------- 21 files changed, 63 insertions(+), 50 deletions(-) diff --git a/modules.json b/modules.json index af6504e5..622f8797 100644 --- a/modules.json +++ b/modules.json @@ -7,82 +7,82 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cutadapt": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "0efbaeb95c58da5a1096c99b5e919bc0c99cc952", "installed_by": ["modules"] }, "epang/place": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "epang/split": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "fastqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "gappa/examineassign": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "gappa/examinegraft": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "gappa/examineheattree": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "hmmer/eslalimask": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "hmmer/eslreformat": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "hmmer/hmmalign": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "hmmer/hmmbuild": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "mafft": { "branch": "master", - "git_sha": "b265b4ff6a35b133b963b4eaddfca0ffb3395236", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["fasta_newick_epang_gappa"] }, "multiqc": { "branch": "master", - "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "vsearch/sintax": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "vsearch/usearchglobal": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] } } @@ -91,7 +91,7 @@ "nf-core": { "fasta_newick_epang_gappa": { "branch": "master", - "git_sha": "6ad90f5583fb375c60a913a24ed1c79339efc019", + "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 800a6099..ebc87273 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -5,7 +5,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index e55b8d43..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,11 +4,10 @@ """Provide functions to merge multiple versions.yml files.""" +import yaml import platform from textwrap import dedent -import yaml - def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/cutadapt/main.nf b/modules/nf-core/cutadapt/main.nf index 45a99ee8..60bd648a 100644 --- a/modules/nf-core/cutadapt/main.nf +++ b/modules/nf-core/cutadapt/main.nf @@ -5,7 +5,7 @@ process CUTADAPT { conda "bioconda::cutadapt=3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' : - 'quay.io/biocontainers/cutadapt:3.4--py39h38f01e4_1' }" + 'biocontainers/cutadapt:3.4--py39h38f01e4_1' }" input: tuple val(meta), path(reads) @@ -34,4 +34,17 @@ process CUTADAPT { cutadapt: \$(cutadapt --version) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def trimmed = meta.single_end ? "${prefix}.trim.fastq.gz" : "${prefix}_1.trim.fastq.gz ${prefix}_2.trim.fastq.gz" + """ + touch ${prefix}.cutadapt.log + touch ${trimmed} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cutadapt: \$(cutadapt --version) + END_VERSIONS + """ } diff --git a/modules/nf-core/cutadapt/meta.yml b/modules/nf-core/cutadapt/meta.yml index bcfe291c..768bac3a 100644 --- a/modules/nf-core/cutadapt/meta.yml +++ b/modules/nf-core/cutadapt/meta.yml @@ -10,7 +10,7 @@ tools: description: | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. documentation: https://cutadapt.readthedocs.io/en/stable/index.html - doi: DOI:10.14806/ej.17.1.200 + doi: 10.14806/ej.17.1.200 licence: ["MIT"] input: - meta: diff --git a/modules/nf-core/epang/place/main.nf b/modules/nf-core/epang/place/main.nf index 35525d31..799acaa1 100644 --- a/modules/nf-core/epang/place/main.nf +++ b/modules/nf-core/epang/place/main.nf @@ -5,7 +5,7 @@ process EPANG_PLACE { conda "bioconda::epa-ng=0.3.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': - 'quay.io/biocontainers/epa-ng:0.3.8--h9a82719_1' }" + 'biocontainers/epa-ng:0.3.8--h9a82719_1' }" input: tuple val(meta), path(queryaln), path(referencealn), path(referencetree) diff --git a/modules/nf-core/epang/split/main.nf b/modules/nf-core/epang/split/main.nf index 973dd6dd..fe372541 100644 --- a/modules/nf-core/epang/split/main.nf +++ b/modules/nf-core/epang/split/main.nf @@ -5,7 +5,7 @@ process EPANG_SPLIT { conda "bioconda::epa-ng=0.3.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1': - 'quay.io/biocontainers/epa-ng:0.3.8--h9a82719_1' }" + 'biocontainers/epa-ng:0.3.8--h9a82719_1' }" input: tuple val(meta), path(refaln), path(fullaln) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9ae58381..07d5e433 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -5,7 +5,7 @@ process FASTQC { conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" + 'biocontainers/fastqc:0.11.9--0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/gappa/examineassign/main.nf b/modules/nf-core/gappa/examineassign/main.nf index 1c48d953..6d920b83 100644 --- a/modules/nf-core/gappa/examineassign/main.nf +++ b/modules/nf-core/gappa/examineassign/main.nf @@ -5,7 +5,7 @@ process GAPPA_EXAMINEASSIGN { conda "bioconda::gappa=0.8.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - 'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }" + 'biocontainers/gappa:0.8.0--h9a82719_0' }" input: tuple val(meta), path(jplace), path(taxonomy) diff --git a/modules/nf-core/gappa/examinegraft/main.nf b/modules/nf-core/gappa/examinegraft/main.nf index b1121f3a..f10aaa31 100644 --- a/modules/nf-core/gappa/examinegraft/main.nf +++ b/modules/nf-core/gappa/examinegraft/main.nf @@ -5,7 +5,7 @@ process GAPPA_EXAMINEGRAFT { conda "bioconda::gappa=0.8.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - 'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }" + 'biocontainers/gappa:0.8.0--h9a82719_0' }" input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/gappa/examineheattree/main.nf b/modules/nf-core/gappa/examineheattree/main.nf index 6898992f..5a6105c0 100644 --- a/modules/nf-core/gappa/examineheattree/main.nf +++ b/modules/nf-core/gappa/examineheattree/main.nf @@ -5,7 +5,7 @@ process GAPPA_EXAMINEHEATTREE { conda "bioconda::gappa=0.8.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0': - 'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }" + 'biocontainers/gappa:0.8.0--h9a82719_0' }" input: tuple val(meta), path(jplace) diff --git a/modules/nf-core/hmmer/eslalimask/main.nf b/modules/nf-core/hmmer/eslalimask/main.nf index 37776430..83ceae4c 100644 --- a/modules/nf-core/hmmer/eslalimask/main.nf +++ b/modules/nf-core/hmmer/eslalimask/main.nf @@ -5,7 +5,7 @@ process HMMER_ESLALIMASK { conda "bioconda::hmmer=3.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + 'biocontainers/hmmer:3.3.2--h1b792b2_1' }" input: tuple val(meta), path(unmaskedaln), val(fmask_rf), val(fmask_all), val(gmask_rf), val(gmask_all), val(pmask_rf), val(pmask_all) diff --git a/modules/nf-core/hmmer/eslreformat/main.nf b/modules/nf-core/hmmer/eslreformat/main.nf index 6eaae099..fd675b79 100644 --- a/modules/nf-core/hmmer/eslreformat/main.nf +++ b/modules/nf-core/hmmer/eslreformat/main.nf @@ -5,7 +5,7 @@ process HMMER_ESLREFORMAT { conda "bioconda::hmmer=3.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1': - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + 'biocontainers/hmmer:3.3.2--h1b792b2_1' }" input: tuple val(meta), path(seqfile) diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf index 63f2bbd1..74e7ee02 100644 --- a/modules/nf-core/hmmer/hmmalign/main.nf +++ b/modules/nf-core/hmmer/hmmalign/main.nf @@ -5,7 +5,7 @@ process HMMER_HMMALIGN { conda "bioconda::hmmer=3.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + 'biocontainers/hmmer:3.3.2--h1b792b2_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 91924b99..1cbe6c95 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -5,7 +5,7 @@ process HMMER_HMMBUILD { conda "bioconda::hmmer=3.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2': - 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }" + 'biocontainers/hmmer:3.3.2--h1b792b2_1' }" input: tuple val(meta), path(alignment) diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf index d2b02b78..420b6484 100644 --- a/modules/nf-core/mafft/main.nf +++ b/modules/nf-core/mafft/main.nf @@ -5,7 +5,7 @@ process MAFFT { conda "bioconda::mafft=7.508" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mafft:7.508--hec16e2b_0': - 'quay.io/biocontainers/mafft:7.508--hec16e2b_0' }" + 'biocontainers/mafft:7.508--hec16e2b_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 4b604749..1fc387be 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,7 +4,7 @@ process MULTIQC { conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/vsearch/sintax/main.nf b/modules/nf-core/vsearch/sintax/main.nf index 273ca698..fb122e1b 100644 --- a/modules/nf-core/vsearch/sintax/main.nf +++ b/modules/nf-core/vsearch/sintax/main.nf @@ -5,7 +5,7 @@ process VSEARCH_SINTAX { conda "bioconda::vsearch=2.21.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - 'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }" + 'biocontainers/vsearch:2.21.1--h95f258a_0' }" input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/main.nf b/modules/nf-core/vsearch/usearchglobal/main.nf index 7ce662ba..8a5e8e90 100644 --- a/modules/nf-core/vsearch/usearchglobal/main.nf +++ b/modules/nf-core/vsearch/usearchglobal/main.nf @@ -5,7 +5,7 @@ process VSEARCH_USEARCHGLOBAL { conda "bioconda::vsearch=2.21.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vsearch:2.21.1--h95f258a_0': - 'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }" + 'biocontainers/vsearch:2.21.1--h95f258a_0' }" input: tuple val(meta), path(queryfasta) diff --git a/modules/nf-core/vsearch/usearchglobal/meta.yml b/modules/nf-core/vsearch/usearchglobal/meta.yml index 3b22e9cd..153d6628 100644 --- a/modules/nf-core/vsearch/usearchglobal/meta.yml +++ b/modules/nf-core/vsearch/usearchglobal/meta.yml @@ -9,9 +9,9 @@ tools: - "vsearch": description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" homepage: "https://github.com/torognes/vsearch" - documentation: "None" + tool_dev_url: "https://github.com/torognes/vsearch" - doi: "doi: 10.7717/peerj.2584" + doi: "10.7717/peerj.2584" licence: "['GPL v3-or-later OR BSD-2-clause']" input: diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml b/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml index a6dbe999..2337aa58 100644 --- a/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml +++ b/subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json name: "fasta_newick_epang_gappa" description: Run phylogenetic placement with a number of query sequences plus a reference alignment and phylogeny. Used in nf-core/phyloplace. keywords: @@ -19,19 +20,19 @@ modules: - gappa/examineheattree input: - ch_pp_data: - type: map - description: | - Structure: [ - meta: val(meta), - data: [ - alignmethod: 'hmmer', - queryseqfile: path("*.faa"), - refseqfile: path("*.alnfaa"), - refphylogeny: path("*.newick"), - model: "LG", - taxonomy: path("*.tsv") + type: map + description: | + Structure: [ + meta: val(meta), + data: [ + alignmethod: 'hmmer', + queryseqfile: path("*.faa"), + refseqfile: path("*.alnfaa"), + refphylogeny: path("*.newick"), + model: "LG", + taxonomy: path("*.tsv") + ] ] - ] - meta: type: map description: | From eeff592036db77ad8f11abeb304fad596bb9854f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:19:40 +0200 Subject: [PATCH 5/9] bump minimal nextflow version + add container registry outside of scopes --- nextflow.config | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 9337c0de..a29f2d8b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -182,7 +182,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -206,7 +205,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -275,6 +273,13 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set default registry for Docker, Singularity and Podman independent of -profile +// Will not be used unless Docker, Singularity and Podman are enabled +// Set to your registry if you have a mirror of containers +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -299,8 +304,8 @@ manifest { homePage = 'https://github.com/nf-core/ampliseq' description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '2.6.0' + nextflowVersion = '!>=23.04.0' + version = '2.6.1' doi = '10.3389/fmicb.2020.550420' } From 1579196bf90d2f9b3af1fa50c65b66941d4b2782 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:21:33 +0200 Subject: [PATCH 6/9] bump minimal nextflow --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b9a5297e..06ad337f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT else - echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT + echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT fi test: From 94d56ae0c9a460a1b738525cbbd154197b25663d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 10:22:32 +0200 Subject: [PATCH 7/9] bump minimal nextflow --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1fb0499a..56e499a3 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1493841-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1493841) [![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-important?labelColor=000000)](https://doi.org/10.3389/fmicb.2020.550420) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) From 2aa1fe07459119d21fd5abb8f01b242a4fca59c3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 12:15:56 +0200 Subject: [PATCH 8/9] update tests.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 b0f87eb2..ff20b72e 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}, 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=2.6.0}}" + "{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}, 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=2.6.1}}" ], "timestamp": "2023-05-28T21:08:54+0000" }, diff --git a/tests/pipeline/fasta.nf.test.snap b/tests/pipeline/fasta.nf.test.snap index e07eaf3d..93c68816 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}, Workflow={nf-core/ampliseq=2.6.0}}" + "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-05-28T21:06:17+0000" }, diff --git a/tests/pipeline/iontorrent.nf.test.snap b/tests/pipeline/iontorrent.nf.test.snap index 17a54c28..3fe42493 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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.6.0}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-06-20T01:42:35+0000" }, diff --git a/tests/pipeline/multi.nf.test.snap b/tests/pipeline/multi.nf.test.snap index a54fb230..82186c6a 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}, QIIME2_INSEQ={qiime2=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.6.0}}" + "{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}, QIIME2_INSEQ={qiime2=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-05-28T21:15:03+0000" }, diff --git a/tests/pipeline/novaseq.nf.test.snap b/tests/pipeline/novaseq.nf.test.snap index 6a9514cf..25dcf446 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=2.6.0}}" + "{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=2.6.1}}" ], "timestamp": "2023-06-20T00:10:02+0000" }, diff --git a/tests/pipeline/pacbio_its.nf.test.snap b/tests/pipeline/pacbio_its.nf.test.snap index 46d609ec..6aacb139 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}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_USEARCHGLOBAL={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.6.0}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, SBDIEXPORT={R=3.6.3}, VSEARCH_USEARCHGLOBAL={vsearch=2.21.1}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-06-20T02:07:02+0000" }, diff --git a/tests/pipeline/pplace.nf.test.snap b/tests/pipeline/pplace.nf.test.snap index e284e31d..10810531 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}, 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=2.6.0}}" + "{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}, 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=2.6.1}}" ], "timestamp": "2023-06-20T17:24:03+0000" }, diff --git a/tests/pipeline/reftaxcustom.nf.test.snap b/tests/pipeline/reftaxcustom.nf.test.snap index 9c21f20e..f1f6527e 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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.6.0}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-05-28T21:18:54+0000" }, diff --git a/tests/pipeline/single.nf.test.snap b/tests/pipeline/single.nf.test.snap index 1a57197d..86d628f1 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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.6.0}}" + "{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}, RENAME_RAW_DATA_FILES={sed=4.7}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-05-28T20:35:33+0000" }, diff --git a/tests/pipeline/sintax.nf.test.snap b/tests/pipeline/sintax.nf.test.snap index a2ff96db..f4ba8fdd 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}, 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=2.6.0}}" + "{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}, 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=2.6.1}}" ], "timestamp": "2023-06-20T16:40:18+0000" }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index dd6ec5fa..11a200cb 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_LEN_ASV={Biostrings=2.58.0, R=4.0.3}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, 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}, Workflow={nf-core/ampliseq=2.6.0}}" + "{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_LEN_ASV={Biostrings=2.58.0, R=4.0.3}, FILTER_STATS={pandas=1.1.5, python=3.9.1}, 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}, Workflow={nf-core/ampliseq=2.6.1}}" ], "timestamp": "2023-05-28T20:55:32+0000" }, From 1c37cb8e7bfbd344c8469ad9170b79df0edfaf41 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 27 Jun 2023 14:24:01 +0200 Subject: [PATCH 9/9] update CHANGELOG --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 90e3e6a8..db3140ab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## nf-core/ampliseq version 2.6.1 - 2023-06-27 + +### `Fixed` + +- [#603](https://github.com/nf-core/ampliseq/pull/603) - Fix all containers registry + ## nf-core/ampliseq version 2.6.0 - 2023-06-27 ### `Added`