From b9d2630334e96623164ab7e8d51e38f28b794382 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Mon, 15 Jul 2024 15:02:59 +0100 Subject: [PATCH 01/16] Added missing when: clause --- modules/local/bamtobed_sort.nf | 3 +++ modules/local/extract_telo.nf | 3 +++ modules/local/find_telomere_regions.nf | 3 +++ modules/local/find_telomere_windows.nf | 3 +++ modules/local/gap_length.nf | 3 +++ modules/local/generate_cram_csv.nf | 3 +++ modules/local/generate_genome_file.nf | 3 +++ modules/local/get_largest_scaff.nf | 3 +++ modules/local/getminmaxpunches.nf | 3 +++ modules/local/reformat_intersect.nf | 3 +++ modules/local/rename_ids.nf | 3 +++ modules/local/replace_dots.nf | 3 +++ 12 files changed, 36 insertions(+) diff --git a/modules/local/bamtobed_sort.nf b/modules/local/bamtobed_sort.nf index 7260ac4..6cae32e 100755 --- a/modules/local/bamtobed_sort.nf +++ b/modules/local/bamtobed_sort.nf @@ -13,6 +13,9 @@ process BAMTOBED_SORT { tuple val(meta), path("*.bed"), emit: sorted_bed path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = args.ext.prefix ?: "${meta.id}" def st_cores = task.cpus > 4 ? 4 : "${task.cpus}" diff --git a/modules/local/extract_telo.nf b/modules/local/extract_telo.nf index cad234f..33f82a9 100755 --- a/modules/local/extract_telo.nf +++ b/modules/local/extract_telo.nf @@ -15,6 +15,9 @@ process EXTRACT_TELO { path("*bedgraph") , emit: bedgraph path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + shell: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. diff --git a/modules/local/find_telomere_regions.nf b/modules/local/find_telomere_regions.nf index 6f0d56c..f34d147 100755 --- a/modules/local/find_telomere_regions.nf +++ b/modules/local/find_telomere_regions.nf @@ -12,6 +12,9 @@ process FIND_TELOMERE_REGIONS { tuple val( meta ), file( "*.telomere" ) , emit: telomere path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. diff --git a/modules/local/find_telomere_windows.nf b/modules/local/find_telomere_windows.nf index 2fcd002..7ff2fe7 100755 --- a/modules/local/find_telomere_windows.nf +++ b/modules/local/find_telomere_windows.nf @@ -15,6 +15,9 @@ process FIND_TELOMERE_WINDOWS { tuple val( meta ), file( "*.windows" ) , emit: windows path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. diff --git a/modules/local/gap_length.nf b/modules/local/gap_length.nf index 54f47df..d2a5dbd 100755 --- a/modules/local/gap_length.nf +++ b/modules/local/gap_length.nf @@ -14,6 +14,9 @@ process GAP_LENGTH { tuple val( meta ), file( "*bedgraph" ) , emit: bed path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + shell: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf index 776287f..aefd5e1 100755 --- a/modules/local/generate_cram_csv.nf +++ b/modules/local/generate_cram_csv.nf @@ -11,6 +11,9 @@ process GENERATE_CRAM_CSV { tuple val(meta), path('*.csv'), emit: csv path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/local/generate_genome_file.nf b/modules/local/generate_genome_file.nf index 233e9ff..c0c0967 100755 --- a/modules/local/generate_genome_file.nf +++ b/modules/local/generate_genome_file.nf @@ -14,6 +14,9 @@ process GENERATE_GENOME_FILE { tuple val( meta ), file( "my.genome" ) , emit: dotgenome path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf index 6348eda..c34e84f 100755 --- a/modules/local/get_largest_scaff.nf +++ b/modules/local/get_largest_scaff.nf @@ -15,6 +15,9 @@ process GET_LARGEST_SCAFF { env largest_scaff , emit: scaff_size path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + shell: def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. $/ diff --git a/modules/local/getminmaxpunches.nf b/modules/local/getminmaxpunches.nf index 7a42e3d..6075547 100755 --- a/modules/local/getminmaxpunches.nf +++ b/modules/local/getminmaxpunches.nf @@ -15,6 +15,9 @@ process GETMINMAXPUNCHES{ tuple val(meta), path ( '*max.bed' ) , optional: true , emit: max path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + shell: def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. $/ diff --git a/modules/local/reformat_intersect.nf b/modules/local/reformat_intersect.nf index 1d1930c..68856db 100755 --- a/modules/local/reformat_intersect.nf +++ b/modules/local/reformat_intersect.nf @@ -13,6 +13,9 @@ process REFORMAT_INTERSECT { output: tuple val( meta ), file( "*.bed" ), emit: bed + when: + task.ext.when == null || task.ext.when + shell: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. diff --git a/modules/local/rename_ids.nf b/modules/local/rename_ids.nf index f69f518..2760999 100755 --- a/modules/local/rename_ids.nf +++ b/modules/local/rename_ids.nf @@ -14,6 +14,9 @@ process RENAME_IDS { tuple val( meta ), file( "*bed" ) , emit: bed path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + shell: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. diff --git a/modules/local/replace_dots.nf b/modules/local/replace_dots.nf index 4d12f5c..5c70ef1 100755 --- a/modules/local/replace_dots.nf +++ b/modules/local/replace_dots.nf @@ -14,6 +14,9 @@ process REPLACE_DOTS { tuple val( meta ), file( "*bed" ), emit: bed path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + shell: def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. From 501572c5bc8341022a3e491f2bf2e5560d366a62 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Mon, 15 Jul 2024 16:30:11 +0100 Subject: [PATCH 02/16] nf-core lint doesn't like double quotes for labels --- modules/local/avgcov.nf | 2 +- modules/local/cram_filter_align_bwamem2_fixmate_sort.nf | 2 +- modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf | 2 +- modules/local/longreadcoveragescalelog.nf | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/avgcov.nf b/modules/local/avgcov.nf index 7e1e477..bbce302 100644 --- a/modules/local/avgcov.nf +++ b/modules/local/avgcov.nf @@ -1,6 +1,6 @@ process AVGCOV { tag "${meta.id}" - label "process_single" + label 'process_single' conda "conda-forge::coreutils=9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf index 64ce6c9..521d901 100755 --- a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf +++ b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf @@ -1,6 +1,6 @@ process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT { tag "$meta.id" - label "process_high" + label 'process_high' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' : diff --git a/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf index 997d886..5070c5e 100644 --- a/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf +++ b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf @@ -1,6 +1,6 @@ process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT { tag "$meta.id" - label "process_high" + label 'process_high' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' : diff --git a/modules/local/longreadcoveragescalelog.nf b/modules/local/longreadcoveragescalelog.nf index 2924146..d54125e 100644 --- a/modules/local/longreadcoveragescalelog.nf +++ b/modules/local/longreadcoveragescalelog.nf @@ -1,6 +1,6 @@ process LONGREADCOVERAGESCALELOG { tag "${meta.id}" - label "process_single" + label 'process_single' conda "conda-forge::python=3.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From f71aeb2275505650631e6f5398c124b56f71510e Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Mon, 15 Jul 2024 16:30:27 +0100 Subject: [PATCH 03/16] "process_tiny" doesn't exist --- modules/local/generate_cram_csv.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf index aefd5e1..01d7873 100755 --- a/modules/local/generate_cram_csv.nf +++ b/modules/local/generate_cram_csv.nf @@ -1,6 +1,6 @@ process GENERATE_CRAM_CSV { tag "${meta.id}" - label 'process_tiny' + label 'process_single' container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' From 01a1b26d7ce3819a52ab08becb542a02674be793 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Mon, 15 Jul 2024 16:43:25 +0100 Subject: [PATCH 04/16] Added notifications that those modules don't support Conda --- modules/local/find_telomere_regions.nf | 5 +++++ modules/local/generate_cram_csv.nf | 5 +++++ modules/local/pretext_graph.nf | 5 +++++ 3 files changed, 15 insertions(+) diff --git a/modules/local/find_telomere_regions.nf b/modules/local/find_telomere_regions.nf index f34d147..a0bf0fc 100755 --- a/modules/local/find_telomere_regions.nf +++ b/modules/local/find_telomere_regions.nf @@ -4,6 +4,11 @@ process FIND_TELOMERE_REGIONS { container 'docker.io/library/gcc:7.1.0' + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "FIND_TELOMERE_REGIONS module does not support Conda. Please use Docker / Singularity instead." + } + input: tuple val( meta ), path( file ) val (telomereseq) diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf index 01d7873..f46c1ce 100755 --- a/modules/local/generate_cram_csv.nf +++ b/modules/local/generate_cram_csv.nf @@ -4,6 +4,11 @@ process GENERATE_CRAM_CSV { container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GENERATE_CRAM_CSV module does not support Conda. Please use Docker / Singularity instead." + } + input: tuple val(meta), path(crampath) diff --git a/modules/local/pretext_graph.nf b/modules/local/pretext_graph.nf index 62b0d8f..7d8832c 100644 --- a/modules/local/pretext_graph.nf +++ b/modules/local/pretext_graph.nf @@ -4,6 +4,11 @@ process PRETEXT_GRAPH { container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3" + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "PRETEXT_GRAPH module does not support Conda. Please use Docker / Singularity instead." + } + input: tuple val(meta), path(pretext_file, stageAs: 'pretext.pretext') tuple val(gap), path(gap_file, stageAs: 'gap.bed') From 68b369b4cfbaf0e430d31c69ea95fd6fcb0a96fb Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Mon, 15 Jul 2024 17:20:23 +0100 Subject: [PATCH 05/16] nf-core doesn't like the whitespace --- modules/local/extract_repeat.nf | 2 +- modules/local/extract_telo.nf | 2 +- modules/local/find_telomere_regions.nf | 2 +- modules/local/find_telomere_windows.nf | 2 +- modules/local/gap_length.nf | 2 +- modules/local/generate_genome_file.nf | 2 +- modules/local/get_largest_scaff.nf | 2 +- modules/local/reformat_intersect.nf | 2 +- modules/local/rename_ids.nf | 2 +- modules/local/replace_dots.nf | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/local/extract_repeat.nf b/modules/local/extract_repeat.nf index 8258a30..2c68ab6 100755 --- a/modules/local/extract_repeat.nf +++ b/modules/local/extract_repeat.nf @@ -8,7 +8,7 @@ process EXTRACT_REPEAT { 'biocontainers/perl:5.26.2' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), path( "*.bed" ) , emit: bed diff --git a/modules/local/extract_telo.nf b/modules/local/extract_telo.nf index 33f82a9..a705521 100755 --- a/modules/local/extract_telo.nf +++ b/modules/local/extract_telo.nf @@ -8,7 +8,7 @@ process EXTRACT_TELO { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), file( "*bed" ) , emit: bed diff --git a/modules/local/find_telomere_regions.nf b/modules/local/find_telomere_regions.nf index a0bf0fc..8a37153 100755 --- a/modules/local/find_telomere_regions.nf +++ b/modules/local/find_telomere_regions.nf @@ -10,7 +10,7 @@ process FIND_TELOMERE_REGIONS { } input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) val (telomereseq) output: diff --git a/modules/local/find_telomere_windows.nf b/modules/local/find_telomere_windows.nf index 7ff2fe7..d2ef584 100755 --- a/modules/local/find_telomere_windows.nf +++ b/modules/local/find_telomere_windows.nf @@ -9,7 +9,7 @@ process FIND_TELOMERE_WINDOWS { 'biocontainers/java-jdk:8.0.112--1' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), file( "*.windows" ) , emit: windows diff --git a/modules/local/gap_length.nf b/modules/local/gap_length.nf index d2a5dbd..386d549 100755 --- a/modules/local/gap_length.nf +++ b/modules/local/gap_length.nf @@ -8,7 +8,7 @@ process GAP_LENGTH { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), file( "*bedgraph" ) , emit: bed diff --git a/modules/local/generate_genome_file.nf b/modules/local/generate_genome_file.nf index c0c0967..dc9e343 100755 --- a/modules/local/generate_genome_file.nf +++ b/modules/local/generate_genome_file.nf @@ -8,7 +8,7 @@ process GENERATE_GENOME_FILE { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( fai ) + tuple val(meta), path(fai) output: tuple val( meta ), file( "my.genome" ) , emit: dotgenome diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf index c34e84f..6746e21 100755 --- a/modules/local/get_largest_scaff.nf +++ b/modules/local/get_largest_scaff.nf @@ -9,7 +9,7 @@ process GET_LARGEST_SCAFF { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: env largest_scaff , emit: scaff_size diff --git a/modules/local/reformat_intersect.nf b/modules/local/reformat_intersect.nf index 68856db..005db04 100755 --- a/modules/local/reformat_intersect.nf +++ b/modules/local/reformat_intersect.nf @@ -8,7 +8,7 @@ process REFORMAT_INTERSECT { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), file( "*.bed" ), emit: bed diff --git a/modules/local/rename_ids.nf b/modules/local/rename_ids.nf index 2760999..02295be 100755 --- a/modules/local/rename_ids.nf +++ b/modules/local/rename_ids.nf @@ -8,7 +8,7 @@ process RENAME_IDS { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), file( "*bed" ) , emit: bed diff --git a/modules/local/replace_dots.nf b/modules/local/replace_dots.nf index 5c70ef1..80ea929 100755 --- a/modules/local/replace_dots.nf +++ b/modules/local/replace_dots.nf @@ -8,7 +8,7 @@ process REPLACE_DOTS { 'docker.io/ubuntu:20.04' }" input: - tuple val( meta ), path( file ) + tuple val(meta), path(file) output: tuple val( meta ), file( "*bed" ), emit: bed From d57f61a704b65ceb1e2eaddc9030d3bd7eabc74b Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 16 Jul 2024 12:08:20 +0100 Subject: [PATCH 06/16] Adding version output to reformat_intersect --- modules/local/reformat_intersect.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/reformat_intersect.nf b/modules/local/reformat_intersect.nf index 005db04..1bb7ab9 100755 --- a/modules/local/reformat_intersect.nf +++ b/modules/local/reformat_intersect.nf @@ -12,6 +12,7 @@ process REFORMAT_INTERSECT { output: tuple val( meta ), file( "*.bed" ), emit: bed + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From d9a5cec31aa0b103627f511cf79479e10d40e812 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 16 Jul 2024 13:13:06 +0100 Subject: [PATCH 07/16] Updated Version Int --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index b82cf8b..ee7a088 100755 --- a/nextflow.config +++ b/nextflow.config @@ -203,7 +203,7 @@ manifest { description = """A simple pipeline to generate pretext files for genomic curation.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0dev' + version = '1.0' doi = '' } From c037750c6180b44f435403541db6c8c7465c818b Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Tue, 16 Jul 2024 16:19:19 +0100 Subject: [PATCH 08/16] Adding citation file and updating version --- CITATION.cff | 31 +++++++++++++++++++++++++++++++ nextflow.config | 2 +- 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..9f9e263 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,31 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: sanger-tol/curationpretext v1.0.0 +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Damon-Lee Bernard + family-names: Pointon + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0003-2949-6719" + - given-names: Matthieu + family-names: Muffato + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0002-7860-3560" + - given-names: Ying + family-names: Sims + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0003-4765-4872" + - given-names: William + family-names: Eagles + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0009-0006-9956-0404" +repository-code: "https://github.com/sanger-tol/curationpretext" +license: MIT +commit: TODO +version: 1.0.0 +date-released: "2024-07-18" \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index ee7a088..259f638 100755 --- a/nextflow.config +++ b/nextflow.config @@ -203,7 +203,7 @@ manifest { description = """A simple pipeline to generate pretext files for genomic curation.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0' + version = '1.0.0' doi = '' } From c733f1556cf6ce6da3f6742ac4bf606d5a83572c Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 17 Jul 2024 09:34:06 +0100 Subject: [PATCH 09/16] Linting fix --- CITATION.cff | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 9f9e263..ead007f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -9,23 +9,23 @@ message: >- type: software authors: - given-names: Damon-Lee Bernard - family-names: Pointon - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0003-2949-6719" + family-names: Pointon + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0003-2949-6719" - given-names: Matthieu - family-names: Muffato - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0002-7860-3560" + family-names: Muffato + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0002-7860-3560" - given-names: Ying - family-names: Sims - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0003-4765-4872" + family-names: Sims + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0003-4765-4872" - given-names: William - family-names: Eagles - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0009-0006-9956-0404" + family-names: Eagles + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0009-0006-9956-0404" repository-code: "https://github.com/sanger-tol/curationpretext" license: MIT commit: TODO version: 1.0.0 -date-released: "2024-07-18" \ No newline at end of file +date-released: "2024-07-18" From 8b72624ca6962bbe794f813365a1541948af977e Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Wed, 17 Jul 2024 12:01:02 +0100 Subject: [PATCH 10/16] Changes to CITATIONS and testing for the tupled env --- CITATION.cff | 27 +++++++++++++++------------ modules/local/get_largest_scaff.nf | 4 ++-- subworkflows/local/accessory_files.nf | 4 ++-- 3 files changed, 19 insertions(+), 16 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index ead007f..8a0ff1c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -9,21 +9,24 @@ message: >- type: software authors: - given-names: Damon-Lee Bernard - family-names: Pointon - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0003-2949-6719" + family-names: Pointon + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0003-2949-6719" - given-names: Matthieu - family-names: Muffato - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0002-7860-3560" + family-names: Muffato + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0002-7860-3560" - given-names: Ying - family-names: Sims - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0003-4765-4872" + family-names: Sims + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0003-4765-4872" - given-names: William - family-names: Eagles - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0009-0006-9956-0404" + family-names: Eagles + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0009-0006-9956-0404" +identifiers: + - type: doi + value: 10.5281/zenodo.XXXXXXX repository-code: "https://github.com/sanger-tol/curationpretext" license: MIT commit: TODO diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf index 6746e21..604db03 100755 --- a/modules/local/get_largest_scaff.nf +++ b/modules/local/get_largest_scaff.nf @@ -12,8 +12,8 @@ process GET_LARGEST_SCAFF { tuple val(meta), path(file) output: - env largest_scaff , emit: scaff_size - path "versions.yml" , emit: versions + tuple val(meta), env(largest_scaff), emit: scaff_size + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when diff --git a/subworkflows/local/accessory_files.nf b/subworkflows/local/accessory_files.nf index f0378bc..a371235 100755 --- a/subworkflows/local/accessory_files.nf +++ b/subworkflows/local/accessory_files.nf @@ -46,7 +46,7 @@ workflow ACCESSORY_FILES { // GAP_FINDER ( reference_tuple, - GET_LARGEST_SCAFF.out.scaff_size.toInteger() + GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[0].toInteger()} ) ch_versions = ch_versions.mix(GAP_FINDER.out.versions) @@ -54,7 +54,7 @@ workflow ACCESSORY_FILES { // SUBWORKFLOW: GENERATE TELOMERE WINDOW FILES WITH LONGREAD READS AND REFERENCE // TELO_FINDER ( - GET_LARGEST_SCAFF.out.scaff_size, + GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[0].toInteger()}, reference_tuple, params.teloseq ) From 716ae6714ac52811ff6b94ebaaef247461158ea0 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 17 Jul 2024 20:13:20 +0100 Subject: [PATCH 11/16] We don't run tests on AWS --- .github/workflows/awsfulltest.yml | 34 ------------------------------- .github/workflows/awstest.yml | 29 -------------------------- 2 files changed, 63 deletions(-) delete mode 100644 .github/workflows/awsfulltest.yml delete mode 100644 .github/workflows/awstest.yml diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml deleted file mode 100644 index b7514c1..0000000 --- a/.github/workflows/awsfulltest.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: nf-core AWS full size tests -# This workflow is triggered on published releases. -# It can be additionally triggered manually with GitHub actions workflow dispatch button. -# It runs the -profile 'test_full' on AWS batch - -on: - release: - types: [published] - workflow_dispatch: -jobs: - run-tower: - name: Run AWS full tests - if: github.repository == 'sanger-tol/curationpretext' - runs-on: ubuntu-latest - steps: - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 - # TODO nf-core: You can customise AWS full pipeline tests as required - # Add full size test data (but still relatively small datasets for few samples) - # on the `test_full.config` test runs with only one set of parameters - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/curationpretext/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/curationpretext/results-${{ github.sha }}" - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: tower_action_*.log diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml deleted file mode 100644 index d1e66bd..0000000 --- a/.github/workflows/awstest.yml +++ /dev/null @@ -1,29 +0,0 @@ -name: nf-core AWS test -# This workflow can be triggered manually with the GitHub actions workflow dispatch button. -# It runs the -profile 'test' on AWS batch - -on: - workflow_dispatch: -jobs: - run-tower: - name: Run AWS tests - if: github.repository == 'sannger-tol/curationpretextt' - runs-on: ubuntu-latest - steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/curationpretext/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/curationpretext/results-test-${{ github.sha }}" - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: tower_action_*.log From 4b3fa6b2d0d42633a486b1ffc39ead52c996e24c Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 17 Jul 2024 20:13:32 +0100 Subject: [PATCH 12/16] Removed badges that are not relevant to us --- README.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/README.md b/README.md index 1f725fc..df95df5 100755 --- a/README.md +++ b/README.md @@ -1,15 +1,10 @@ # ![sanger-tol/curationpretext](docs/images/curationpretext-light.png#gh-light-mode-only) ![sanger-tol/curationpretext](docs/images/curationpretext-dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/curationpretext/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) - [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](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/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/sanger-tol/curationpretext) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23curationpretext-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/curationpretext)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) - ## Introduction **sanger-tol/curationpretext** is a bioinformatics pipeline typically used in conjunction with [TreeVal](https://github.com/sanger-tol/treeval) to generate pretext maps (and optionally telomeric, gap, coverage, and repeat density plots which can be ingested into pretext) for the manual curation of high quality genomes. From 43c7a6eacc4212c5141bd6ee502990d1ad5dac92 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 17 Jul 2024 20:14:42 +0100 Subject: [PATCH 13/16] We run prettier, not EditorConfig on .cff files --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3f27dab..5f1b621 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -22,7 +22,7 @@ jobs: run: npm install -g editorconfig-checker - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') + run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') Prettier: runs-on: ubuntu-latest From fe29d8aefafeecc7a5e755c81b3420c025088a88 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 17 Jul 2024 20:16:17 +0100 Subject: [PATCH 14/16] Empty block --- README.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/README.md b/README.md index df95df5..0ac7686 100755 --- a/README.md +++ b/README.md @@ -133,7 +133,3 @@ You can cite the `nf-core` publication as follows: > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). - -``` - -``` From 887526786e5bae12f8f563f1c61195a7647f307f Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 17 Jul 2024 20:17:15 +0100 Subject: [PATCH 15/16] CITATIONS.md already exists --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index 0ac7686..32dc1f2 100755 --- a/README.md +++ b/README.md @@ -122,8 +122,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `# - - An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: From 353325b937065d0c31582f9aa53b6cab2fb24a97 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 17 Jul 2024 20:28:26 +0100 Subject: [PATCH 16/16] bugfix: the value is in the second element (the first one is meta) --- subworkflows/local/accessory_files.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/accessory_files.nf b/subworkflows/local/accessory_files.nf index a371235..d14a7ea 100755 --- a/subworkflows/local/accessory_files.nf +++ b/subworkflows/local/accessory_files.nf @@ -46,7 +46,7 @@ workflow ACCESSORY_FILES { // GAP_FINDER ( reference_tuple, - GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[0].toInteger()} + GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[1].toInteger()} ) ch_versions = ch_versions.mix(GAP_FINDER.out.versions) @@ -54,7 +54,7 @@ workflow ACCESSORY_FILES { // SUBWORKFLOW: GENERATE TELOMERE WINDOW FILES WITH LONGREAD READS AND REFERENCE // TELO_FINDER ( - GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[0].toInteger()}, + GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[1].toInteger()}, reference_tuple, params.teloseq ) @@ -93,4 +93,4 @@ workflow ACCESSORY_FILES { half_bed = LONGREAD_COVERAGE.out.ch_halfbed maxs_bed = LONGREAD_COVERAGE.out.ch_maxbed versions = ch_versions.ifEmpty(null) -} \ No newline at end of file +}