From 184ed21c51441e02674dad4f4d6b9aba642cbf3a Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 15:14:25 +0100 Subject: [PATCH 1/7] add additional inputs instead of params usage subwf --- modules/local/count_rna/main.nf | 6 ++-- modules/local/count_rna/meta.yml | 6 ++++ subworkflows/local/genome_evaluation.nf | 40 +++++++++++++------------ subworkflows/local/rna_detection.nf | 8 +++-- workflows/genomesubmit.nf | 10 +++++-- 5 files changed, 44 insertions(+), 26 deletions(-) diff --git a/modules/local/count_rna/main.nf b/modules/local/count_rna/main.nf index ebd4154..ca9876e 100644 --- a/modules/local/count_rna/main.nf +++ b/modules/local/count_rna/main.nf @@ -11,6 +11,8 @@ process COUNT_RNA { input: tuple val(meta), path(trnas_stats), path(rrna_gff) + val min_trna_count + val min_rrna_percentage output: tuple val(meta), path("*rna_decision.tsv"), emit: rna_decision @@ -22,8 +24,8 @@ process COUNT_RNA { --trna ${trnas_stats} \\ --rrna ${rrna_gff} \\ --name ${meta.id} \\ - --trna-limit ${params.trna_limit} \\ - --rrna-limit ${params.rrna_limit} \\ + --trna-limit ${min_trna_count} \\ + --rrna-limit ${min_rrna_percentage} \\ --output ${meta.id}_rna_decision.tsv cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/count_rna/meta.yml b/modules/local/count_rna/meta.yml index 5cbb5fa..d7e92f9 100644 --- a/modules/local/count_rna/meta.yml +++ b/modules/local/count_rna/meta.yml @@ -30,6 +30,12 @@ input: type: file description: rRNA annotation file from barrnap (GFF3 format) pattern: "*.gff" + - min_trna_count: + type: value + description: Minimum required number of tRNA genes. + - min_rrna_percentage: + type: value + description: Minimum required percentage coverage for each rRNA subunit. output: - meta: diff --git a/subworkflows/local/genome_evaluation.nf b/subworkflows/local/genome_evaluation.nf index 6eb4fd9..16d872e 100644 --- a/subworkflows/local/genome_evaluation.nf +++ b/subworkflows/local/genome_evaluation.nf @@ -20,7 +20,11 @@ include { CHECKM2_PREDICT } from '../../modules/nf-core/checkm2/predict workflow GENOME_EVALUATION { take: - ch_fasta // channel: [ val(meta), path(fasta) ] + ch_fasta // channel: [ val(meta), path(fasta) ] + ch_checkm2_db // channel: [ val(meta), path(db) ] - pre-built db as directory + // provide channel.empty() to trigger automatic download via ch_checkm2_db_zenodo_id + ch_checkm2_db_zenodo_id // channel: [ val(meta), val(db_id) ] - db ID for CHECKM2_DATABASEDOWNLOAD (e.g. '1234567') + // only used if ch_checkm2_db is empty main: ch_versions = channel.empty() @@ -29,24 +33,20 @@ workflow GENOME_EVALUATION { // Database preparation // - if (!params.checkm2_db || !file(params.checkm2_db).exists()) { - // Conditional download: only trigger if ch_fasta has items - ch_download_trigger = ch_fasta - .map { _meta, _fasta -> params.checkm2_db_zenodo_id } - .first() // Only need one trigger regardless of how many fasta files + // Download and prepare db from scratch if no pre-built db provided + // Only trigger if ch_fasta has items + ch_download_trigger = ch_checkm2_db + .count() + .filter { count -> count == 0 } // Only proceed if ch_checkm2_db is empty + .combine(ch_fasta.first()) + .combine(ch_checkm2_db_zenodo_id) + .map { _count, _meta, _fasta, db_meta, db_id -> [db_meta, db_id] } - CHECKM2_DATABASEDOWNLOAD(ch_download_trigger) - ch_checkm2_db = CHECKM2_DATABASEDOWNLOAD.out.database - } - else { - // Use existing database - ch_checkm2_db = channel.of( - [ - [id: "checkm2_db"], - file(params.checkm2_db), - ] - ) - } + CHECKM2_DATABASEDOWNLOAD(ch_download_trigger) + ch_versions = ch_versions.mix( CHECKM2_DATABASEDOWNLOAD.out.versions ) + + // Combine db sources - one of these channels will be empty depending on inputs + ch_db = ch_checkm2_db.mix(CHECKM2_DATABASEDOWNLOAD.out.database).first() // // Genome evaluation @@ -54,11 +54,13 @@ workflow GENOME_EVALUATION { CHECKM2_PREDICT( ch_fasta, - ch_checkm2_db, + ch_db, ) + ch_versions = ch_versions.mix( CHECKM2_PREDICT.out.versions ) emit: genome_evaluation = CHECKM2_PREDICT.out.checkm2_tsv // channel: [ val(meta), path(tsv) ] stats_versions = CHECKM2_PREDICT.out.versions_checkm2_predict + versions = ch_versions } diff --git a/subworkflows/local/rna_detection.nf b/subworkflows/local/rna_detection.nf index d0130f6..85a83e5 100644 --- a/subworkflows/local/rna_detection.nf +++ b/subworkflows/local/rna_detection.nf @@ -20,7 +20,9 @@ include { TRNASCANSE } from '../../modules/nf-core/trnascanse' workflow RNA_DETECTION { take: - fasta + fasta // channel: [ val(meta), path(fasta) ] + min_trna_count // val: int - minimum number of tRNAs required to pass MIMAG standard (e.g. 18) + min_rrna_percentage // val: float - minimum percentage of rRNA genes required to pass MIMAG standard (e.g. 75) main: @@ -36,7 +38,9 @@ workflow RNA_DETECTION { ch_versions = ch_versions.mix( TRNASCANSE.out.versions ) COUNT_RNA( - TRNASCANSE.out.stats.join(BARRNAP.out.gff) + TRNASCANSE.out.stats.join(BARRNAP.out.gff), + min_trna_count, + min_rrna_percentage ) ch_versions = ch_versions.mix( COUNT_RNA.out.versions ) diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index a17299c..404a005 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -129,7 +129,9 @@ workflow GENOMESUBMIT { .set { branched_rna_results } RNA_DETECTION ( - branched_rna_results.rna_prediction_input + branched_rna_results.rna_prediction_input, + params.trna_limit, + params.rrna_limit ) ch_versions = ch_versions.mix( RNA_DETECTION.out.versions ) @@ -152,7 +154,9 @@ workflow GENOMESUBMIT { .set { branched_stats_results } GENOME_EVALUATION ( - branched_stats_results.genome_evaluation_input + branched_stats_results.genome_evaluation_input, + params.checkm2_db, + params.checkm2_db_zenodo_id ) // Create a value channel with the version string @@ -283,7 +287,7 @@ workflow GENOMESUBMIT { CREATE_MANIFESTS( fasta_updated_with_stats.map{meta, fasta -> fasta}.collect(), genome_metadata_csv, - params.mode, // mags or bins + mags_or_bins_flag, // mags or bins study_accession_ch.first() ) From 4843e6200a2055d945a8826a19768d6aa0aaef1d Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 15:27:52 +0100 Subject: [PATCH 2/7] add additional inputs instead of params usage in ENA_WEBIN_CLI_WRAPPER --- modules/local/ena_webin_cli_wrapper/main.nf | 10 +++--- modules/local/ena_webin_cli_wrapper/meta.yml | 35 ++++++++++++++------ workflows/assemblysubmit.nf | 4 ++- workflows/genomesubmit.nf | 4 ++- 4 files changed, 36 insertions(+), 17 deletions(-) diff --git a/modules/local/ena_webin_cli_wrapper/main.nf b/modules/local/ena_webin_cli_wrapper/main.nf index 7918ce1..b3a33b2 100644 --- a/modules/local/ena_webin_cli_wrapper/main.nf +++ b/modules/local/ena_webin_cli_wrapper/main.nf @@ -11,16 +11,18 @@ process ENA_WEBIN_CLI_WRAPPER { input: tuple val(meta), path(submission_item), path(manifest) path(webin_cli_jar) + val test_upload + val webincli_submit output: tuple val(meta), path("*_accessions.tsv"), emit: accessions path "versions.yml", emit: versions script: - def args = task.ext.args ?: "" - def prefix = task.ext.prefix ?: "${meta.id}" - def test_flag = params.test_upload ? "--test" : "" - def submit_or_validate = params.webincli_submit ? "--mode submit": "--mode validate" + def args = task.ext.args ?: "" + def prefix = task.ext.prefix ?: "${meta.id}" + def test_flag = test_upload ? "--test" : "" + def submit_or_validate = webincli_submit ? "--mode submit": "--mode validate" """ # change FASTA path in manifest to current workdir diff --git a/modules/local/ena_webin_cli_wrapper/meta.yml b/modules/local/ena_webin_cli_wrapper/meta.yml index a0abd93..042e073 100644 --- a/modules/local/ena_webin_cli_wrapper/meta.yml +++ b/modules/local/ena_webin_cli_wrapper/meta.yml @@ -31,19 +31,32 @@ input: type: file description: | The Webin-CLI JAR file downloaded by ena_webin_cli_download. - pattern: "webin-cli-*.jar" + pattern: "webin-cli-*.jar" + - - test_upload: + type: value + description: Whether to run ENA Webin-CLI in test mode. + - webincli_submit: + type: value + description: Whether to submit (`true`) or only validate (`false`). output: - - - accessions: - type: file - description: | - TSV file containing the accession assigned by ENA for the submitted item. - File has two columns: "alias" and "accession". - - - versions: - - "versions.yml": - type: file - description: File containing software versions. - pattern: "versions.yml" + - accessions: + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1' ]` + - "*_accessions.tsv": + type: file + description: | + TSV file containing the accession assigned by ENA for the submitted item. + File has two columns: "alias" and "accession". + pattern: "*_accessions.tsv" + - versions: + - "versions.yml": + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@KateSakharova" diff --git a/workflows/assemblysubmit.nf b/workflows/assemblysubmit.nf index 5743f7d..de2b7d5 100644 --- a/workflows/assemblysubmit.nf +++ b/workflows/assemblysubmit.nf @@ -174,7 +174,9 @@ workflow ASSEMBLYSUBMIT { SUBMIT ( assemblies_with_coverage.join(GENERATE_ASSEMBLY_MANIFEST.out.manifest), - ENA_WEBIN_CLI_DOWNLOAD.out.webin_cli_jar + ENA_WEBIN_CLI_DOWNLOAD.out.webin_cli_jar, + params.test_upload, + params.webincli_submit ) // diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index 404a005..80437f5 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -318,7 +318,9 @@ workflow GENOMESUBMIT { SUBMIT ( ch_combined, - ENA_WEBIN_CLI_DOWNLOAD.out.webin_cli_jar + ENA_WEBIN_CLI_DOWNLOAD.out.webin_cli_jar, + params.test_upload, + params.webincli_submit ) // From 43f02f25d5d79102c987702c9df3336640914068 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 15:48:23 +0100 Subject: [PATCH 3/7] add additional inputs in GENOME_UPLOAD --- modules/local/genome_upload/main.nf | 16 +++++++++------ modules/local/genome_upload/meta.yml | 30 ++++++++++++++++++---------- workflows/genomesubmit.nf | 6 +++++- 3 files changed, 34 insertions(+), 18 deletions(-) diff --git a/modules/local/genome_upload/main.nf b/modules/local/genome_upload/main.nf index 221e8fe..645d65f 100644 --- a/modules/local/genome_upload/main.nf +++ b/modules/local/genome_upload/main.nf @@ -9,6 +9,10 @@ process GENOME_UPLOAD { path(table_for_upload) val(mags_or_bins_flag) val(submission_study) + val(centre_name) + val(is_tpa) + val(upload_force) + val(test_upload) output: path "results/{MAG,bin}_upload/manifests*/*.manifest" , emit: manifests @@ -22,16 +26,16 @@ process GENOME_UPLOAD { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def tpa = params.upload_tpa ? "--tpa" : "" - def force = params.upload_force ? "--force" : "" - def mode = (!params.test_upload) ? "--live" : "" + def args = task.ext.args ?: '' + def tpa = is_tpa ? "--tpa" : "" + def force = upload_force ? "--force" : "" + def mode = (!test_upload) ? "--live" : "" """ genome_upload \\ - -u $submission_study \\ + -u ${submission_study} \\ --genome_info ${table_for_upload} \\ - --centre_name $params.centre_name \\ + --centre_name ${centre_name} \\ --${mags_or_bins_flag} \\ ${tpa} \\ ${force} \\ diff --git a/modules/local/genome_upload/meta.yml b/modules/local/genome_upload/meta.yml index 0a33443..ae631a1 100644 --- a/modules/local/genome_upload/meta.yml +++ b/modules/local/genome_upload/meta.yml @@ -13,11 +13,6 @@ tools: documentation: https://github.com/EBI-Metagenomics/genome_uploader licence: ["Apache License"] input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - table_for_upload: type: file description: | @@ -26,16 +21,29 @@ input: type: file description: File in FASTA format containing targeted mag/bin/assembly for submission pattern: "*.{fasta,fna,fas,fa}*" + - mags_or_bins_flag: + type: value + description: Upload mode selector. Expected values are `mags` or `bins`. + - submission_study: + type: value + description: ENA study accession used for submission. + - centre_name: + type: value + description: Submitting centre name required by ENA. + - is_tpa: + type: value + description: Whether genomes are submitted as TPA (Third Party Annotation). + - upload_force: + type: value + description: Whether to force rewrite existing cache of ENA metadata. + - test_upload: + type: value + description: Whether to run in ENA test mode. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - manifests: type: file - description: Maniseft file required for submission with webin-cli + description: Manifest file required for submission with webin-cli pattern: "*.manifest" - ena_upload_backup_json: type: file diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index 80437f5..b57cd3e 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -288,7 +288,11 @@ workflow GENOMESUBMIT { fasta_updated_with_stats.map{meta, fasta -> fasta}.collect(), genome_metadata_csv, mags_or_bins_flag, // mags or bins - study_accession_ch.first() + study_accession_ch.first(), + params.centre_name, + params.upload_tpa, + params.upload_force, + params.test_upload ) // All manifests were generated in one run From 3a6bd172ed8f05cb90308953dd8717651f932d4f Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 15:49:26 +0100 Subject: [PATCH 4/7] add additional inputs in GENERATE_ASSEMBLY_MANIFEST --- modules/local/generate_assembly_manifest/main.nf | 3 ++- modules/local/generate_assembly_manifest/meta.yml | 3 +++ workflows/assemblysubmit.nf | 3 ++- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/modules/local/generate_assembly_manifest/main.nf b/modules/local/generate_assembly_manifest/main.nf index fcaf32f..aefc0a7 100644 --- a/modules/local/generate_assembly_manifest/main.nf +++ b/modules/local/generate_assembly_manifest/main.nf @@ -7,6 +7,7 @@ process GENERATE_ASSEMBLY_MANIFEST { input: tuple val(meta), path(assembly_fasta), path(data_csv) val(assembly_study) + val(is_tpa) output: tuple val(meta), path("${assembly_study}_upload/*.manifest") , emit: manifest @@ -18,7 +19,7 @@ process GENERATE_ASSEMBLY_MANIFEST { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def tpa = params.upload_tpa ? "--tpa" : "" + def tpa = is_tpa ? "--tpa" : "" """ assembly_manifest \\ --study ${assembly_study} \\ diff --git a/modules/local/generate_assembly_manifest/meta.yml b/modules/local/generate_assembly_manifest/meta.yml index da69a3b..2d58258 100644 --- a/modules/local/generate_assembly_manifest/meta.yml +++ b/modules/local/generate_assembly_manifest/meta.yml @@ -31,6 +31,9 @@ input: description: | Pre-existing study ID to submit to if available. Must exist in the webin account. + - is_tpa: + type: value + description: Whether assembly being submitted is a TPA (Third Party Annotation). output: - meta: diff --git a/workflows/assemblysubmit.nf b/workflows/assemblysubmit.nf index de2b7d5..146506f 100644 --- a/workflows/assemblysubmit.nf +++ b/workflows/assemblysubmit.nf @@ -165,7 +165,8 @@ workflow ASSEMBLYSUBMIT { // Generate assembly manifest files and submit them to ENA GENERATE_ASSEMBLY_MANIFEST( assemblies_with_coverage.join(assembly_metadata_csv), - study_accession_ch.first() + study_accession_ch.first(), + params.upload_tpa ) ENA_WEBIN_CLI_DOWNLOAD ( From 2505af4b7d3a3b505247958bdc35ef92f17dbd54 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 17:24:46 +0100 Subject: [PATCH 5/7] update tests --- modules/local/count_rna/tests/main.nf.test | 4 ++++ modules/local/ena_webin_cli_wrapper/meta.yml | 2 +- modules/local/generate_assembly_manifest/tests/main.nf.test | 2 ++ 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/modules/local/count_rna/tests/main.nf.test b/modules/local/count_rna/tests/main.nf.test index dbb8543..e687fbb 100644 --- a/modules/local/count_rna/tests/main.nf.test +++ b/modules/local/count_rna/tests/main.nf.test @@ -16,6 +16,8 @@ nextflow_process { file("$moduleDir/tests/data/ecoli.stats", checkIfExists: true), file("$moduleDir/tests/data/ecoli_bac.gff", checkIfExists: true) ] + input[1] = 18 + input[2] = 80 """ } } @@ -49,6 +51,8 @@ nextflow_process { file("$moduleDir/tests/data/ecoli.stats", checkIfExists: true), file("$moduleDir/tests/data/ecoli_bac.gff", checkIfExists: true) ] + input[1] = 18 + input[2] = 80 """ } } diff --git a/modules/local/ena_webin_cli_wrapper/meta.yml b/modules/local/ena_webin_cli_wrapper/meta.yml index 042e073..ee7993d 100644 --- a/modules/local/ena_webin_cli_wrapper/meta.yml +++ b/modules/local/ena_webin_cli_wrapper/meta.yml @@ -35,7 +35,7 @@ input: - - test_upload: type: value description: Whether to run ENA Webin-CLI in test mode. - - webincli_submit: + - - webincli_submit: type: value description: Whether to submit (`true`) or only validate (`false`). diff --git a/modules/local/generate_assembly_manifest/tests/main.nf.test b/modules/local/generate_assembly_manifest/tests/main.nf.test index 2b96eae..22fea31 100644 --- a/modules/local/generate_assembly_manifest/tests/main.nf.test +++ b/modules/local/generate_assembly_manifest/tests/main.nf.test @@ -18,6 +18,7 @@ nextflow_process { file(params.pipelines_testdata_base_path + "/samplesheets/samplesheet_generatemanifest.csv", checkIfExists: true) ] input[1] = "PRJ12345" + input[2] = false """ } @@ -62,6 +63,7 @@ nextflow_process { file('test_samplesheet_generatemanifest.csv') ] input[1] = "PRJ12345" + input[2] = false """ } } From e726c1e1c20187be1263cc7b066403ecbfd09b9e Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 17:54:00 +0100 Subject: [PATCH 6/7] fix checkm2_db definition --- subworkflows/local/genome_evaluation.nf | 3 --- workflows/genomesubmit.nf | 13 +++++++++++-- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/genome_evaluation.nf b/subworkflows/local/genome_evaluation.nf index 16d872e..1324339 100644 --- a/subworkflows/local/genome_evaluation.nf +++ b/subworkflows/local/genome_evaluation.nf @@ -43,7 +43,6 @@ workflow GENOME_EVALUATION { .map { _count, _meta, _fasta, db_meta, db_id -> [db_meta, db_id] } CHECKM2_DATABASEDOWNLOAD(ch_download_trigger) - ch_versions = ch_versions.mix( CHECKM2_DATABASEDOWNLOAD.out.versions ) // Combine db sources - one of these channels will be empty depending on inputs ch_db = ch_checkm2_db.mix(CHECKM2_DATABASEDOWNLOAD.out.database).first() @@ -56,11 +55,9 @@ workflow GENOME_EVALUATION { ch_fasta, ch_db, ) - ch_versions = ch_versions.mix( CHECKM2_PREDICT.out.versions ) emit: genome_evaluation = CHECKM2_PREDICT.out.checkm2_tsv // channel: [ val(meta), path(tsv) ] stats_versions = CHECKM2_PREDICT.out.versions_checkm2_predict - versions = ch_versions } diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index b57cd3e..2b47c3b 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -153,10 +153,19 @@ workflow GENOMESUBMIT { } .set { branched_stats_results } + // build input structures for CheckM2 DB depending on what provided as input + def checkm2_db_input = params.checkm2_db + ? channel.of( [['id': 'CHECKM2_DB'], file(params.checkm2_db)] ) + : channel.empty() + + def checkm2_db_id_input = (!params.checkm2_db && params.checkm2_db_download_id) + ? channel.of( [['id': 'CHECKM2_DB_id'], params.checkm2_db_download_id] ) + : channel.empty() + GENOME_EVALUATION ( branched_stats_results.genome_evaluation_input, - params.checkm2_db, - params.checkm2_db_zenodo_id + checkm2_db_input, + checkm2_db_id_input ) // Create a value channel with the version string From b3afab59859cddeeb9f36adf52ed3ab991f02f53 Mon Sep 17 00:00:00 2001 From: Sofia Ochkalova Date: Fri, 24 Apr 2026 18:05:38 +0100 Subject: [PATCH 7/7] remove --upload_force param because it's unnecessary for a user --- conf/modules.config | 1 + modules/local/genome_upload/main.nf | 3 --- modules/local/genome_upload/meta.yml | 3 --- nextflow.config | 2 -- nextflow_schema.json | 8 +------- workflows/genomesubmit.nf | 1 - 6 files changed, 2 insertions(+), 16 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 7f87441..39d2e37 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -145,6 +145,7 @@ process { // withName: 'GENOME_UPLOAD' { + ext.args = "--force" // ensures that ENA metadata is re-downloaded even if cache exists publishDir = [ path: { "${params.outdir}/${params.mode}/upload/manifests" }, mode: params.publish_dir_mode, diff --git a/modules/local/genome_upload/main.nf b/modules/local/genome_upload/main.nf index 645d65f..0000d25 100644 --- a/modules/local/genome_upload/main.nf +++ b/modules/local/genome_upload/main.nf @@ -11,7 +11,6 @@ process GENOME_UPLOAD { val(submission_study) val(centre_name) val(is_tpa) - val(upload_force) val(test_upload) output: @@ -28,7 +27,6 @@ process GENOME_UPLOAD { script: def args = task.ext.args ?: '' def tpa = is_tpa ? "--tpa" : "" - def force = upload_force ? "--force" : "" def mode = (!test_upload) ? "--live" : "" """ @@ -38,7 +36,6 @@ process GENOME_UPLOAD { --centre_name ${centre_name} \\ --${mags_or_bins_flag} \\ ${tpa} \\ - ${force} \\ ${mode} \\ --out results \\ ${args} diff --git a/modules/local/genome_upload/meta.yml b/modules/local/genome_upload/meta.yml index ae631a1..d04f33a 100644 --- a/modules/local/genome_upload/meta.yml +++ b/modules/local/genome_upload/meta.yml @@ -33,9 +33,6 @@ input: - is_tpa: type: value description: Whether genomes are submitted as TPA (Third Party Annotation). - - upload_force: - type: value - description: Whether to force rewrite existing cache of ENA metadata. - test_upload: type: value description: Whether to run in ENA test mode. diff --git a/nextflow.config b/nextflow.config index 21871a0..7807171 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,8 +16,6 @@ params { submission_study = null centre_name = null upload_tpa = false - // TODO: remove this parameter because it will never be used, and update the genome_uploader module accordingly - upload_force = true test_upload = true webincli_submit = true webin_cli_version = "9.0.3" diff --git a/nextflow_schema.json b/nextflow_schema.json index 9f52527..155039d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -292,12 +292,6 @@ "default": true, "help": "Use that flag for development purposes or for validation of your submissions. Submission would be done to TEST ENA server instead of LIVE server. TEST server holds data 24h and removes afterwords. LIVE server does not have option to modify your submission, you can only suppress data and re-upload" }, - "upload_force": { - "type": "boolean", - "description": "Enables force mode for genome_uploader (used for MAGs/BINs submission)", - "default": true, - "help": "Forces reset of bin/MAG sample xmls generation. This is useful if you changed something in your tsv table, or if ENA metadata haven't been downloaded correctly (you can check this in ENA_backup.json). Default: true" - }, "submission_study": { "type": "string", "description": "ENA study accession (PRJ/ERP) to submit the data to", @@ -319,7 +313,7 @@ }, "webin_cli_version": { "type": "string", - "description": "Version of webon-cli.jar to use for submission", + "description": "Version of webin-cli.jar to use for submission", "default": "9.0.3", "help": "Check version https://github.com/enasequence/webin-cli" } diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index 2b47c3b..a17e809 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -300,7 +300,6 @@ workflow GENOMESUBMIT { study_accession_ch.first(), params.centre_name, params.upload_tpa, - params.upload_force, params.test_upload )