From abd8f513523d5444c9f4dc5670c58ac6adc87539 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 4 Nov 2024 13:58:34 +1300 Subject: [PATCH 01/11] Moved around test_full options --- conf/test_full.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 818e1c86..9ac77972 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -33,13 +33,13 @@ params { ncbi_fcs_gx_tax_id = 35717 // ncbi_fcs_gx_db_path = 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/r2023-01-24' + tidk_skip = false + tidk_repeat_seq = 'TTTGGG' + busco_skip = false busco_mode = 'genome' busco_lineage_datasets = 'fungi_odb10 hypocreales_odb10' - tidk_skip = false - tidk_repeat_seq = 'TTTGGG' - lai_skip = false kraken2_skip = true // Skipping this step as the dataset is humengous (126 GB). Please download the dataset manually @@ -47,10 +47,10 @@ params { hic = 'SRR8238190' + merqury_skip = false + synteny_skip = false synteny_mummer_skip = false synteny_plotsr_skip = false synteny_xref_assemblies = 'https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/dev/assets/xrefsheet.csv' - - merqury_skip = false } From c7998d66923e683601f738908f0e6918519e4e4a Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 4 Nov 2024 14:12:25 +1300 Subject: [PATCH 02/11] Updated pfr params --- nextflow.config | 8 +++----- pfr/params.json | 17 ++++++++++------- 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/nextflow.config b/nextflow.config index 0e7c24bb..6541924c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -9,8 +9,10 @@ // Global default params, used in configs params { - // Input options + // Input/output options input = null + outdir = null + email = null // Validation options check_sequence_duplicates = true @@ -77,10 +79,6 @@ params { // OrthoFinder options orthofinder_skip = true - // Output options - outdir = null - email = null - // Boilerplate options publish_dir_mode = 'copy' email_on_fail = null diff --git a/pfr/params.json b/pfr/params.json index aabf5fba..5d99f9e5 100644 --- a/pfr/params.json +++ b/pfr/params.json @@ -1,5 +1,7 @@ { "input": "/workspace/assemblyqc/testdata/v2/assemblysheet.csv", + "outdir": "./results", + "email": null, "check_sequence_duplicates": true, "assemblathon_stats_n_limit": 100, "gfastats_skip": false, @@ -9,14 +11,14 @@ "ncbi_fcs_gx_tax_id": 3750, "ncbi_fcs_gx_db_path": "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24", "contamination_stops_pipeline": false, - "busco_skip": false, - "busco_mode": "genome", - "busco_lineage_datasets": "embryophyta_odb10 eudicots_odb10", - "busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc", "tidk_skip": false, "tidk_repeat_seq": "TTTAGGG", "tidk_filter_by_size": true, "tidk_filter_size_bp": 1000000, + "busco_skip": false, + "busco_mode": "genome", + "busco_lineage_datasets": "embryophyta_odb10 eudicots_odb10", + "busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc", "lai_skip": false, "kraken2_skip": false, "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314", @@ -24,6 +26,9 @@ "hic_skip_fastp": false, "hic_skip_fastqc": false, "hic_fastp_ext_args": "--qualified_quality_phred 20 --length_required 50", + "hic_samtools_ext_args": "-F 3852", + "merqury_skip": false, + "merqury_kmer_length": 21, "synteny_skip": false, "synteny_mummer_skip": false, "synteny_plotsr_skip": false, @@ -37,7 +42,5 @@ "synteny_color_by_contig": true, "synteny_plotsr_seq_label": "Chr", "synteny_plotsr_assembly_order": "gddh13_v1p1 m9_v1 m9_v1_h1 m9_v1_h2", - "merqury_skip": false, - "outdir": "./results", - "email": null + "orthofinder_skip": false } From 8fcc5ce1929177448ce9064127469b481cc7dcc5 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 4 Nov 2024 14:22:54 +1300 Subject: [PATCH 03/11] Updated pfr_assembly launch script --- conf/test_full.config | 2 +- pfr_assemblyqc | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 9ac77972..5f9580e4 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -43,7 +43,7 @@ params { lai_skip = false kraken2_skip = true // Skipping this step as the dataset is humengous (126 GB). Please download the dataset manually - // kraken2_db_path = 'https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240112.tar.gz' + // kraken2_db_path = 'https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240904.tar.gz' hic = 'SRR8238190' diff --git a/pfr_assemblyqc b/pfr_assemblyqc index 62c34a3f..52ad7dee 100644 --- a/pfr_assemblyqc +++ b/pfr_assemblyqc @@ -27,7 +27,7 @@ shift $((OPTIND -1)) ml unload perl ml apptainer/1.1 -ml nextflow/23.04.4 +ml nextflow/24.04.3 export TMPDIR="/workspace/$USER/tmp" export APPTAINER_BINDPATH="$APPTAINER_BINDPATH,$TMPDIR:$TMPDIR,$TMPDIR:/tmp" From cf11c1bd93b4437413078ce3c4b2f94ab5ed0d6a Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 4 Nov 2024 20:13:58 +1300 Subject: [PATCH 04/11] Version bump and a couple of minor fixes --- .github/version_checks.sh | 2 ++ CHANGELOG.md | 2 +- CITATION.cff | 2 +- modules/local/generatekaryotype.nf | 7 ++----- nextflow.config | 2 +- 5 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/version_checks.sh b/.github/version_checks.sh index e7b1a90a..3acfa8d6 100755 --- a/.github/version_checks.sh +++ b/.github/version_checks.sh @@ -1,5 +1,7 @@ #!/usr/bin/env bash +set -euo pipefail + config_version=$(sed -n "/^\s*version\s*=\s*'/s/version//p" nextflow.config | tr -d "=[:space:]'") cff_version=$(sed -n '/^version: /s/version: //p' CITATION.cff | tr -d '[:space:]') diff --git a/CHANGELOG.md b/CHANGELOG.md index 5203d463..9a9f8205 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.2.0dev - [04-Nov-2024] +## v2.2.0 - [04-Nov-2024] ### `Added` diff --git a/CITATION.cff b/CITATION.cff index 37a9c841..18bb4b7d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -25,7 +25,7 @@ authors: - family-names: "Deng" given-names: "Cecilia" title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality" -version: 2.2.0dev +version: 2.2.0 date-released: 2024-07-30 url: "https://github.com/Plant-Food-Research-Open/assemblyqc" doi: 10.1093/bioinformatics/btae477 diff --git a/modules/local/generatekaryotype.nf b/modules/local/generatekaryotype.nf index e3771fe6..94cd4f64 100644 --- a/modules/local/generatekaryotype.nf +++ b/modules/local/generatekaryotype.nf @@ -35,8 +35,7 @@ process GENERATEKARYOTYPE { exit 0 fi - tmp_file=\$(mktemp) - printf '%s\\n' "\${ref_seqs[@]}" > "\$tmp_file" + printf '%s\\n' "\${ref_seqs[@]}" > ${target_on_ref}.${seq_tag}.tmp if [[ $seq_tag = "all" ]];then cat $target_seq_len > filtered.target.seq.len @@ -45,7 +44,7 @@ process GENERATEKARYOTYPE { fi cat filtered.target.seq.len | awk '{print \$1,\$2,"grey"}' OFS="\\t" > colored.filtered.target.seq.len - grep -w -f "\$tmp_file" $ref_seq_len > filtered.ref.seq.len + grep -w -f ${target_on_ref}.${seq_tag}.tmp $ref_seq_len > filtered.ref.seq.len cat filtered.ref.seq.len | awk '{print \$1,\$2,"black"}' OFS="\\t" > colored.filtered.ref.seq.len cat colored.filtered.ref.seq.len | sort -k1V > merged.seq.lengths @@ -67,8 +66,6 @@ process GENERATEKARYOTYPE { | sed '/^\$/d' \ | awk '{print "chr -",\$1,\$1,"0",\$2-1,\$3}' OFS="\\t" \ > karyotype_target.tsv - - rm "\$tmp_file" """ stub: diff --git a/nextflow.config b/nextflow.config index 6541924c..0677fb0d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -274,7 +274,7 @@ manifest { description = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '2.2.0dev' + version = '2.2.0' doi = 'https://doi.org/10.1093/bioinformatics/btae477' } From af5c449b3c65fca7dd0c9ddf0dde4ea48e86b832 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 4 Nov 2024 21:57:06 +1300 Subject: [PATCH 05/11] Updated PFR's Kraken 2 database to k2_pluspfp_20240904 --- CHANGELOG.md | 1 + docs/usage.md | 2 +- pfr/params.json | 2 +- pfr_assemblyqc | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a9f8205..e05122f4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 10. Updated the tube map along with the tool list [#166](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/166) 11. Added Orthofinder [#167](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/167) 12. Changed order of tool options in the `nextflow.config` file +13. Updated PFR's Kraken 2 database to `k2_pluspfp_20240904` [#170](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/170) ### `Fixed` diff --git a/docs/usage.md b/docs/usage.md index 02b198b3..dd38f31f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -65,7 +65,7 @@ BUSCO lineage databases are downloaded and updated by the BUSCO tool itself. A p ### Kraken 2 -Path to Kraken 2 database is provided by the `kraken2_db_path` parameter. This can be a URL to a public `.tar.gz` file such as `https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240112.tar.gz`. The pipeline can download and extract the database. This is not the recommended practice owing to the size of the database. Rather, the database should be downloaded, extracted and stored in a read-only location. The path to that location can be provided by the `kraken2_db_path` parameter such as `/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314`. +Path to Kraken 2 database is provided by the `kraken2_db_path` parameter. This can be a URL to a public `.tar.gz` file such as `https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_20240112.tar.gz`. The pipeline can download and extract the database. This is not the recommended practice owing to the size of the database. Rather, the database should be downloaded, extracted and stored in a read-only location. The path to that location can be provided by the `kraken2_db_path` parameter such as `/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904`. ## Other parameters diff --git a/pfr/params.json b/pfr/params.json index 5d99f9e5..8b4f0625 100644 --- a/pfr/params.json +++ b/pfr/params.json @@ -21,7 +21,7 @@ "busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc", "lai_skip": false, "kraken2_skip": false, - "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314", + "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904", "hic": null, "hic_skip_fastp": false, "hic_skip_fastqc": false, diff --git a/pfr_assemblyqc b/pfr_assemblyqc index 52ad7dee..b860ae42 100644 --- a/pfr_assemblyqc +++ b/pfr_assemblyqc @@ -40,7 +40,7 @@ if [ $full_test_flag -eq 1 ]; then --ncbi_fcs_gx_skip false \ --ncbi_fcs_gx_db_path "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24" \ --kraken2_skip false \ - --kraken2_db_path "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20230314" \ + --kraken2_db_path "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904" \ -resume \ --outdir results else From e14050942418575723fe6fa1199d17acf9ab971c Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 5 Nov 2024 11:29:50 +1300 Subject: [PATCH 06/11] Increased memory requirement for Kraken 2 to 256.GB --- CHANGELOG.md | 3 ++- conf/base.config | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e05122f4..dec4217f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.2.0 - [04-Nov-2024] +## v2.2.0 - [05-Nov-2024] ### `Added` @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 11. Added Orthofinder [#167](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/167) 12. Changed order of tool options in the `nextflow.config` file 13. Updated PFR's Kraken 2 database to `k2_pluspfp_20240904` [#170](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/170) +14. Increased memory requirement for Kraken 2 to `256.GB` ### `Fixed` diff --git a/conf/base.config b/conf/base.config index f13b4759..e39fbece 100644 --- a/conf/base.config +++ b/conf/base.config @@ -61,7 +61,7 @@ process { memory = { 512.GB * task.attempt } } withName:KRAKEN2 { - memory = { 200.GB * task.attempt } + memory = { 256.GB * task.attempt } } withName:BWA_MEM { time = { 2.day * task.attempt } From d98384a2266b026feffc0a06abdde3534c15743b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 5 Nov 2024 11:56:12 +1300 Subject: [PATCH 07/11] Updated docs and removed resource limits from test_full --- conf/test_full.config | 8 -------- docs/usage.md | 2 +- local_assemblyqc | 1 + 3 files changed, 2 insertions(+), 9 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 5f9580e4..f2ad3d1a 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,14 +10,6 @@ ---------------------------------------------------------------------------------------- */ -process { - resourceLimits = [ - cpus: 10, - memory: '32.GB', - time: '6.h' - ] -} - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index dd38f31f..3090d3c5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -129,7 +129,7 @@ The data for these examples comes from: [umd.edu](https://obj.umiacs.umd.edu/mar All the modules have been tested to work on a single machine with 10 CPUs + 32 GBs of memory, except NCBI FCS GX and Kraken2. Their minimum requirements are: - NCBI FCS GX: 1 CPU + 512 GBs memory -- Kraken2: 1 CPU + 200 GBs memory +- Kraken2: 1 CPU + 250 GBs memory ## Running the pipeline diff --git a/local_assemblyqc b/local_assemblyqc index bcfff8c3..3a211c34 100755 --- a/local_assemblyqc +++ b/local_assemblyqc @@ -17,6 +17,7 @@ nextflow run \ -profile docker,test_full \ -resume \ $stub \ + -c ../nxf-config/resources.config \ --ncbi_fcs_gx_skip false \ --ncbi_fcs_gx_db_path ../dbs/gxdb/test \ --busco_download_path ../dbs/busco \ From 0da7cea5f4a0d04af7ba4a5ce536fb6a30532250 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 5 Nov 2024 12:07:31 +1300 Subject: [PATCH 08/11] Updated synteny_mummer_min_bundle_size for pfr/params --- pfr/params.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pfr/params.json b/pfr/params.json index 8b4f0625..a4062925 100644 --- a/pfr/params.json +++ b/pfr/params.json @@ -37,7 +37,7 @@ "synteny_mummer_plot_type": "both", "synteny_mummer_m2m_align": false, "synteny_mummer_max_gap": 1000000, - "synteny_mummer_min_bundle_size": 1000, + "synteny_mummer_min_bundle_size": 1000000, "synteny_plot_1_vs_all": false, "synteny_color_by_contig": true, "synteny_plotsr_seq_label": "Chr", From e6b968fe0df22fac2f9cdba05d6d0fc2a8003a55 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 5 Nov 2024 16:41:04 +1300 Subject: [PATCH 09/11] Now using _JAVA_OPTIONS in module RUNASSEMBLYVISUALIZER to avoid user preferences related errors --- CHANGELOG.md | 1 + modules/local/runassemblyvisualizer.nf | 10 ++-------- 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dec4217f..1c5def16 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 1. Fixed a bug where Gene score distribution graph did not appear correctly [#125](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/125) 2. Increased memory requirement for `DNADIFF` to avoid SLURM OOM kills with exit code 2 [#141](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/141) 3. Documented the use explicit use of `-revision` parameter [#160](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/160) +4. Now using `_JAVA_OPTIONS` in module `RUNASSEMBLYVISUALIZER` to avoid user preferences related errors ### `Dependencies` diff --git a/modules/local/runassemblyvisualizer.nf b/modules/local/runassemblyvisualizer.nf index 5452dfd0..d52bc590 100644 --- a/modules/local/runassemblyvisualizer.nf +++ b/modules/local/runassemblyvisualizer.nf @@ -21,14 +21,9 @@ process RUNASSEMBLYVISUALIZER { assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g') file_name="${agp_assembly_file}" - cp -r /usr/src/3d-dna/ \\ - 3d-dna + export _JAVA_OPTIONS="-Djava.util.prefs.userRoot=user_prefs -Xms${avail_mem}g -Xmx${avail_mem}g" - sed -i \\ - 's/-Xms49152m -Xmx49152m/-Xms${avail_mem}g -Xmx${avail_mem}g/1' \\ - 3d-dna/visualize/juicebox_tools.sh - - 3d-dna/visualize/run-assembly-visualizer.sh \\ + /usr/src/3d-dna/visualize/run-assembly-visualizer.sh \\ -p false \\ $agp_assembly_file $sorted_links_txt_file @@ -42,7 +37,6 @@ process RUNASSEMBLYVISUALIZER { stub: if ( !task.memory ) { error '[RUNASSEMBLYVISUALIZER] Available memory not known. Specify process memory requirements to fix this.' } - def avail_mem = (task.memory.giga*0.8).intValue() """ assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g') touch "\${assembly_tag}.hic" From 0f9a4eebbf39ae4dda11227ad38db38afdcebca2 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 5 Nov 2024 17:37:36 +1300 Subject: [PATCH 10/11] Now added user.home property to JAVA_OPTIONS --- modules/local/runassemblyvisualizer.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/runassemblyvisualizer.nf b/modules/local/runassemblyvisualizer.nf index d52bc590..e4ca50a4 100644 --- a/modules/local/runassemblyvisualizer.nf +++ b/modules/local/runassemblyvisualizer.nf @@ -21,7 +21,8 @@ process RUNASSEMBLYVISUALIZER { assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g') file_name="${agp_assembly_file}" - export _JAVA_OPTIONS="-Djava.util.prefs.userRoot=user_prefs -Xms${avail_mem}g -Xmx${avail_mem}g" + mkdir user_home + export _JAVA_OPTIONS="-Djava.util.prefs.userRoot=user_prefs -Duser.home=user_home -Xms${avail_mem}g -Xmx${avail_mem}g" /usr/src/3d-dna/visualize/run-assembly-visualizer.sh \\ -p false \\ From ddc9aae8d9612d5aed6173defc00f23a48632048 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 5 Nov 2024 20:44:26 +1300 Subject: [PATCH 11/11] Fixed version mismatches --- docs/usage.md | 2 +- tests/README.md | 2 +- tests/hicparam/main.nf.test.snap | 2 +- tests/invalid/main.nf.test.snap | 2 +- tests/minimal/main.nf.test.snap | 2 +- tests/noltr/main.nf.test.snap | 2 +- tests/orthofinder/main.nf.test.snap | 4 ++-- tests/stub/main.nf.test.snap | 2 +- tests/tiny/main.nf.test.snap | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 3090d3c5..8590c615 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -129,7 +129,7 @@ The data for these examples comes from: [umd.edu](https://obj.umiacs.umd.edu/mar All the modules have been tested to work on a single machine with 10 CPUs + 32 GBs of memory, except NCBI FCS GX and Kraken2. Their minimum requirements are: - NCBI FCS GX: 1 CPU + 512 GBs memory -- Kraken2: 1 CPU + 250 GBs memory +- Kraken2: 1 CPU + 256 GBs memory ## Running the pipeline diff --git a/tests/README.md b/tests/README.md index 6f09f846..a9af91a8 100644 --- a/tests/README.md +++ b/tests/README.md @@ -20,7 +20,7 @@ The GitHub [CI action](../.github/workflows/ci.yml) included with the pipeline c ## Testing with a Large Dataset at Plant&Food -Before each release, the functionality of the entire pipeline is tested with a large dataset on the on-prem SLURM-based HPC at The New Zealand Institute of Plant and Food Research. +Before each release, the functionality of the entire pipeline is tested with a large dataset on the on-prem SLURM-based HPC at The New Zealand Institute for Plant and Food Research. ## Testing Merqury Datasets diff --git a/tests/hicparam/main.nf.test.snap b/tests/hicparam/main.nf.test.snap index feebbdbc..db89beee 100644 --- a/tests/hicparam/main.nf.test.snap +++ b/tests/hicparam/main.nf.test.snap @@ -68,7 +68,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [ diff --git a/tests/invalid/main.nf.test.snap b/tests/invalid/main.nf.test.snap index 9aa72f46..c29b15ad 100644 --- a/tests/invalid/main.nf.test.snap +++ b/tests/invalid/main.nf.test.snap @@ -35,7 +35,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [ diff --git a/tests/minimal/main.nf.test.snap b/tests/minimal/main.nf.test.snap index 44a5d9fc..8e139a7e 100644 --- a/tests/minimal/main.nf.test.snap +++ b/tests/minimal/main.nf.test.snap @@ -35,7 +35,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [ diff --git a/tests/noltr/main.nf.test.snap b/tests/noltr/main.nf.test.snap index 75ee9f5f..d1580b9d 100644 --- a/tests/noltr/main.nf.test.snap +++ b/tests/noltr/main.nf.test.snap @@ -50,7 +50,7 @@ "seqkit": "v2.8.0" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [ diff --git a/tests/orthofinder/main.nf.test.snap b/tests/orthofinder/main.nf.test.snap index 633b6c30..4d34b485 100644 --- a/tests/orthofinder/main.nf.test.snap +++ b/tests/orthofinder/main.nf.test.snap @@ -41,7 +41,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [ @@ -80,4 +80,4 @@ }, "timestamp": "2024-11-01T14:11:21.865104" } -} \ No newline at end of file +} diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap index 74b3740e..d2e05d4c 100644 --- a/tests/stub/main.nf.test.snap +++ b/tests/stub/main.nf.test.snap @@ -230,7 +230,7 @@ "untar": 1.34 }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [ diff --git a/tests/tiny/main.nf.test.snap b/tests/tiny/main.nf.test.snap index 60dfdbbe..b937e1d4 100644 --- a/tests/tiny/main.nf.test.snap +++ b/tests/tiny/main.nf.test.snap @@ -29,7 +29,7 @@ "pigz": "2.3.4" }, "Workflow": { - "plant-food-research-open/assemblyqc": "v2.2.0dev" + "plant-food-research-open/assemblyqc": "v2.2.0" } }, "stable paths": [