From 12678863e9c88934568391bbc53e8da4589ac29d Mon Sep 17 00:00:00 2001 From: Sam Sims Date: Wed, 29 Oct 2025 14:19:02 +0000 Subject: [PATCH 1/8] tests(ena_webin_cli): adds test for the ENA_WEBIN_CLI process tests both validate and push functionality in seperate test. --- modules/local/ena_webin_cli/main.nf.test | 86 +++++++++++++++++++ modules/local/ena_webin_cli/main.nf.test.snap | 26 ++++++ modules/local/ena_webin_cli/setup_test.nf | 17 ++++ 3 files changed, 129 insertions(+) create mode 100644 modules/local/ena_webin_cli/main.nf.test create mode 100644 modules/local/ena_webin_cli/main.nf.test.snap create mode 100644 modules/local/ena_webin_cli/setup_test.nf diff --git a/modules/local/ena_webin_cli/main.nf.test b/modules/local/ena_webin_cli/main.nf.test new file mode 100644 index 0000000..4db38c6 --- /dev/null +++ b/modules/local/ena_webin_cli/main.nf.test @@ -0,0 +1,86 @@ +nextflow_process { + + name "Test Process ENA_WEBIN_CLI" + script "modules/local/ena_webin_cli/main.nf" + process "ENA_WEBIN_CLI" + + test("Run validate with no failures") { + + when { + params { + webincli_submit = false + } + process { + """ + input[0] = Channel.of( + tuple( + [id: 'lachnospira_eligens'], + file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz", checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/lachnospira_eligens.manifest", checkIfExists: true) + ) + ) + """ + } + } + + then { + assertAll { + assert process.success + assert process.out.upload_status[0][1] == 'success' + assert path(process.out.webin_report[0][1]).readLines()[0].contains("Submission(s) validated successfully") + assert snapshot(process.out.versions).match() + } + } + + } + + test("Run push with no failures") { + setup { + run("GENERATE_TEST_DATA") { + script "./setup_test.nf" + process { + """ + input[0] = Channel.of( + file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/lachnospira_eligens.manifest", checkIfExists: true) + ) + """ + } + } + + } + + when { + params { + webincli_submit = true + test_upload = true + } + process { + """ + def fasta = file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz", checkIfExists: true) + + input[0] = GENERATE_TEST_DATA.out.test_manifest.map { manifest -> + tuple( + [id: 'lachnospira_eligens'], + fasta, + file(manifest) + ) + } + """ + } + } + + then { + assertAll { + assert process.success + assert process.out.upload_status[0][1] == 'success' + assert snapshot(process.out.versions).match() + assert path(process.out.webin_report[0][1]).readLines()[1].contains("Submission(s) validated successfully") + assert path(process.out.webin_report[0][1]).readLines()[5].contains("The submission has been completed successfully") + assert path(process.out.webin_report[0][1]).readLines()[6].contains("This was a TEST submission(s)") + + } + } + + } + +} diff --git a/modules/local/ena_webin_cli/main.nf.test.snap b/modules/local/ena_webin_cli/main.nf.test.snap new file mode 100644 index 0000000..ef27c95 --- /dev/null +++ b/modules/local/ena_webin_cli/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "Run validate with no failures": { + "content": [ + [ + "versions.yml:md5,a38fb03bead632d71062a101d7889ded" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-29T14:09:00.202532371" + }, + "Run push with no failures": { + "content": [ + [ + "versions.yml:md5,a38fb03bead632d71062a101d7889ded" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-29T14:01:42.491885321" + } +} \ No newline at end of file diff --git a/modules/local/ena_webin_cli/setup_test.nf b/modules/local/ena_webin_cli/setup_test.nf new file mode 100644 index 0000000..3791b0f --- /dev/null +++ b/modules/local/ena_webin_cli/setup_test.nf @@ -0,0 +1,17 @@ +process GENERATE_TEST_DATA { + label 'process_low' + container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1" + + input: + path(manifest_template) + + output: + path("*.manifest"), emit: test_manifest + + script: + """ + timestamp="\$(date +%s)" + + sed -E "s/^(ASSEMBLYNAME\t[^\t]+)/\\1_\${timestamp}/" "${manifest_template}" > "lachnospira_eligens_dynamic_fixture.manifest" + """ +} From 8a3ea7426929eeba067590d8ae53149aef3669a3 Mon Sep 17 00:00:00 2001 From: Sam Sims Date: Wed, 29 Oct 2025 14:19:27 +0000 Subject: [PATCH 2/8] fix(ena_webin_cli): add status check for validate mode --- modules/local/ena_webin_cli/main.nf | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/modules/local/ena_webin_cli/main.nf b/modules/local/ena_webin_cli/main.nf index 25b12f4..21ad914 100644 --- a/modules/local/ena_webin_cli/main.nf +++ b/modules/local/ena_webin_cli/main.nf @@ -53,6 +53,10 @@ process ENA_WEBIN_CLI { # there was attempt to re-submit already submitted genome export STATUS="success" true + elif grep -q "Submission(s) validated successfully" "${prefix}_webin-cli.report"; then + # we ran with -validate flag + export STATUS="success" + true else export STATUS="failed" false From 449f45409ef00f281a8e4fe0dc743eda09c58657 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 29 Oct 2025 18:10:10 +0000 Subject: [PATCH 3/8] [automated] Fix code linting --- modules/local/ena_webin_cli/setup_test.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/ena_webin_cli/setup_test.nf b/modules/local/ena_webin_cli/setup_test.nf index 3791b0f..9b71031 100644 --- a/modules/local/ena_webin_cli/setup_test.nf +++ b/modules/local/ena_webin_cli/setup_test.nf @@ -1,7 +1,7 @@ process GENERATE_TEST_DATA { label 'process_low' container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1" - + input: path(manifest_template) From ca49cdc85bb2843daa1d6c436ebd7113c43f685a Mon Sep 17 00:00:00 2001 From: "Juan F. Mosquera" Date: Thu, 2 Apr 2026 16:41:44 +0100 Subject: [PATCH 4/8] initial version of ena-webin-cli mocking for tests --- modules/local/ena_webin_cli/main.nf | 39 ++++++++++++++++++------ modules/local/ena_webin_cli/main.nf.test | 21 ++++++++++--- 2 files changed, 47 insertions(+), 13 deletions(-) diff --git a/modules/local/ena_webin_cli/main.nf b/modules/local/ena_webin_cli/main.nf index 21ad914..979614b 100644 --- a/modules/local/ena_webin_cli/main.nf +++ b/modules/local/ena_webin_cli/main.nf @@ -5,8 +5,10 @@ process ENA_WEBIN_CLI { container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1" stageInMode 'copy' - secret 'WEBIN_ACCOUNT' - secret 'WEBIN_PASSWORD' + if (!params.webincli_mock) { + secret 'WEBIN_ACCOUNT' + secret 'WEBIN_PASSWORD' + } input: tuple val(meta), path(submission_item), path(manifest) @@ -23,19 +25,38 @@ process ENA_WEBIN_CLI { def prefix = task.ext.prefix ?: "${meta.id}" def mode = params.test_upload ? "-test" : "" def submit_or_validate = params.webincli_submit ? "-submit": "-validate" + def webincli_mock = params.webincli_mock ? "true" : "false" """ # change FASTA path in manifest to current workdir export ITEM_FULL_PATH=\$(readlink -f ${submission_item}) sed 's|^FASTA\t.*|FASTA\t'"\${ITEM_FULL_PATH}"'|g' ${manifest} > ${prefix}_updated_manifest.manifest - ena-webin-cli \\ - -context=genome \\ - -manifest=${prefix}_updated_manifest.manifest \\ - -userName="\${WEBIN_ACCOUNT}" \\ - -password="\${WEBIN_PASSWORD}" \\ - ${submit_or_validate} \\ - ${mode} + if [[ "${webincli_mock}" == "true" ]]; then + if [[ "${submit_or_validate}" == "-submit" ]]; then + cat <<-EOF > webin-cli.report + INFO : MOCK WEBIN RUN + INFO : command=ena-webin-cli -context=genome -manifest=${prefix}_updated_manifest.manifest ${submit_or_validate} ${mode} + INFO : Submission(s) validated successfully + INFO : The submission has been completed successfully + INFO : This was a TEST submission(s) + EOF + else + cat <<-EOF > webin-cli.report + INFO : MOCK WEBIN RUN + INFO : command=ena-webin-cli -context=genome -manifest=${prefix}_updated_manifest.manifest ${submit_or_validate} ${mode} + INFO : Submission(s) validated successfully + EOF + fi + else + ena-webin-cli \\ + -context=genome \\ + -manifest=${prefix}_updated_manifest.manifest \\ + -userName="\${WEBIN_ACCOUNT}" \\ + -password="\${WEBIN_PASSWORD}" \\ + ${submit_or_validate} \\ + ${mode} + fi mv webin-cli.report "${prefix}_webin-cli.report" diff --git a/modules/local/ena_webin_cli/main.nf.test b/modules/local/ena_webin_cli/main.nf.test index 4db38c6..02de213 100644 --- a/modules/local/ena_webin_cli/main.nf.test +++ b/modules/local/ena_webin_cli/main.nf.test @@ -9,6 +9,7 @@ nextflow_process { when { params { webincli_submit = false + webincli_mock = true } process { """ @@ -27,7 +28,12 @@ nextflow_process { assertAll { assert process.success assert process.out.upload_status[0][1] == 'success' - assert path(process.out.webin_report[0][1]).readLines()[0].contains("Submission(s) validated successfully") + def report_lines = path(process.out.webin_report[0][1]).readLines() + assert report_lines.any { it.contains("MOCK WEBIN RUN") } + assert report_lines.any { it.contains("-context=genome") } + assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") } + assert report_lines.any { it.contains("-validate") } + assert report_lines.any { it.contains("Submission(s) validated successfully") } assert snapshot(process.out.versions).match() } } @@ -53,6 +59,7 @@ nextflow_process { params { webincli_submit = true test_upload = true + webincli_mock = true } process { """ @@ -73,10 +80,16 @@ nextflow_process { assertAll { assert process.success assert process.out.upload_status[0][1] == 'success' + def report_lines = path(process.out.webin_report[0][1]).readLines() + assert report_lines.any { it.contains("MOCK WEBIN RUN") } + assert report_lines.any { it.contains("-context=genome") } + assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") } + assert report_lines.any { it.contains("-submit") } + assert report_lines.any { it.contains("-test") } + assert report_lines.any { it.contains("Submission(s) validated successfully") } + assert report_lines.any { it.contains("The submission has been completed successfully") } + assert report_lines.any { it.contains("This was a TEST submission(s)") } assert snapshot(process.out.versions).match() - assert path(process.out.webin_report[0][1]).readLines()[1].contains("Submission(s) validated successfully") - assert path(process.out.webin_report[0][1]).readLines()[5].contains("The submission has been completed successfully") - assert path(process.out.webin_report[0][1]).readLines()[6].contains("This was a TEST submission(s)") } } From 5e2c41c25d82f0538236f8fe5f3c46b8160f55db Mon Sep 17 00:00:00 2001 From: "Juan F. Mosquera" Date: Sat, 4 Apr 2026 14:45:27 +0100 Subject: [PATCH 5/8] define ena-webin-cli mock and mount it properly for docker and local testing --- modules/local/ena_webin_cli/main.nf | 34 +++-------- modules/local/ena_webin_cli/main.nf.test | 2 +- modules/local/ena_webin_cli/nextflow.config | 12 ++++ .../ena_webin_cli/test-mocking/ena-webin-cli | 60 +++++++++++++++++++ .../test-mocking/mock_submit.report | 5 ++ .../test-mocking/mock_validate.report | 3 + 6 files changed, 89 insertions(+), 27 deletions(-) create mode 100644 modules/local/ena_webin_cli/nextflow.config create mode 100755 modules/local/ena_webin_cli/test-mocking/ena-webin-cli create mode 100644 modules/local/ena_webin_cli/test-mocking/mock_submit.report create mode 100644 modules/local/ena_webin_cli/test-mocking/mock_validate.report diff --git a/modules/local/ena_webin_cli/main.nf b/modules/local/ena_webin_cli/main.nf index 979614b..b82a08a 100644 --- a/modules/local/ena_webin_cli/main.nf +++ b/modules/local/ena_webin_cli/main.nf @@ -5,6 +5,7 @@ process ENA_WEBIN_CLI { container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1" stageInMode 'copy' + // Require authentication secrets for real runs, but not for mock testing. if (!params.webincli_mock) { secret 'WEBIN_ACCOUNT' secret 'WEBIN_PASSWORD' @@ -25,38 +26,19 @@ process ENA_WEBIN_CLI { def prefix = task.ext.prefix ?: "${meta.id}" def mode = params.test_upload ? "-test" : "" def submit_or_validate = params.webincli_submit ? "-submit": "-validate" - def webincli_mock = params.webincli_mock ? "true" : "false" """ # change FASTA path in manifest to current workdir export ITEM_FULL_PATH=\$(readlink -f ${submission_item}) sed 's|^FASTA\t.*|FASTA\t'"\${ITEM_FULL_PATH}"'|g' ${manifest} > ${prefix}_updated_manifest.manifest - if [[ "${webincli_mock}" == "true" ]]; then - if [[ "${submit_or_validate}" == "-submit" ]]; then - cat <<-EOF > webin-cli.report - INFO : MOCK WEBIN RUN - INFO : command=ena-webin-cli -context=genome -manifest=${prefix}_updated_manifest.manifest ${submit_or_validate} ${mode} - INFO : Submission(s) validated successfully - INFO : The submission has been completed successfully - INFO : This was a TEST submission(s) - EOF - else - cat <<-EOF > webin-cli.report - INFO : MOCK WEBIN RUN - INFO : command=ena-webin-cli -context=genome -manifest=${prefix}_updated_manifest.manifest ${submit_or_validate} ${mode} - INFO : Submission(s) validated successfully - EOF - fi - else - ena-webin-cli \\ - -context=genome \\ - -manifest=${prefix}_updated_manifest.manifest \\ - -userName="\${WEBIN_ACCOUNT}" \\ - -password="\${WEBIN_PASSWORD}" \\ - ${submit_or_validate} \\ - ${mode} - fi + ena-webin-cli \ + -context=genome \ + -manifest=${prefix}_updated_manifest.manifest \ + -userName="\${WEBIN_ACCOUNT}" \ + -password="\${WEBIN_PASSWORD}" \ + ${submit_or_validate} \ + ${mode} mv webin-cli.report "${prefix}_webin-cli.report" diff --git a/modules/local/ena_webin_cli/main.nf.test b/modules/local/ena_webin_cli/main.nf.test index 02de213..d84dbd4 100644 --- a/modules/local/ena_webin_cli/main.nf.test +++ b/modules/local/ena_webin_cli/main.nf.test @@ -1,8 +1,8 @@ nextflow_process { - name "Test Process ENA_WEBIN_CLI" script "modules/local/ena_webin_cli/main.nf" process "ENA_WEBIN_CLI" + config "./nextflow.config" test("Run validate with no failures") { diff --git a/modules/local/ena_webin_cli/nextflow.config b/modules/local/ena_webin_cli/nextflow.config new file mode 100644 index 0000000..910e90b --- /dev/null +++ b/modules/local/ena_webin_cli/nextflow.config @@ -0,0 +1,12 @@ +params.testDataDir = "${projectDir}/modules/local/ena_webin_cli/test-mocking" +env { + WEBIN_ACCOUNT = "mock_account" + WEBIN_PASSWORD = "mock_password" + PATH = "${params.testDataDir}:\$PATH" + WEBINCLI_MOCK_TEMPLATE_DIR = "${params.testDataDir}" +} +process { + withName: 'ENA_WEBIN_CLI' { + containerOptions = "-v ${params.testDataDir}:${params.testDataDir}" + } +} diff --git a/modules/local/ena_webin_cli/test-mocking/ena-webin-cli b/modules/local/ena_webin_cli/test-mocking/ena-webin-cli new file mode 100755 index 0000000..fa67290 --- /dev/null +++ b/modules/local/ena_webin_cli/test-mocking/ena-webin-cli @@ -0,0 +1,60 @@ +#!/usr/bin/env bash +# Mock ena-webin-cli script for testing without credentials. +set -euo pipefail + +# Verify that a real ena-webin-cli exists somewhere in PATH beyond this mock. +real_bin="$(which -a ena-webin-cli 2>/dev/null | grep -v "$(realpath "$0")" | head -1 || true)" +if [[ -z "$real_bin" ]]; then + echo "FATAL: No real ena-webin-cli found in PATH besides this mock." >&2 + exit 666 +fi + +# Outputs the version of the real ena-webin-cli when called with -version, to allow testing of version parsing logic. +if [[ "${1:-}" == "-version" ]]; then + echo $(${real_bin} -version 2>&1) + exit 0 +fi + +manifest="" +action="" +mode="" + +for arg in "$@"; do + case "$arg" in + -manifest=*) + manifest="${arg#-manifest=}" + ;; + -submit|-validate) + action="$arg" + ;; + -test) + mode="$arg" + ;; + esac +done + +if [[ -z "$manifest" || -z "$action" ]]; then + echo "Mock ena-webin-cli: missing required arguments" >&2 + exit 1 +fi + +prefix="$(basename "$manifest")" +prefix="${prefix%_updated_manifest.manifest}" + +template_dir="${WEBINCLI_MOCK_TEMPLATE_DIR:-.}" +if [[ "$action" == "-submit" ]]; then + template="$template_dir/mock_submit.report" +else + template="$template_dir/mock_validate.report" +fi + +if [[ ! -f "$template" ]]; then + echo "Mock template file not found: $template" >&2 + exit 1 +fi + +sed \ + -e "s||$prefix|g" \ + -e "s||$action|g" \ + -e "s||$mode|g" \ + "$template" > webin-cli.report diff --git a/modules/local/ena_webin_cli/test-mocking/mock_submit.report b/modules/local/ena_webin_cli/test-mocking/mock_submit.report new file mode 100644 index 0000000..692b300 --- /dev/null +++ b/modules/local/ena_webin_cli/test-mocking/mock_submit.report @@ -0,0 +1,5 @@ +INFO : MOCK WEBIN RUN +INFO : command=ena-webin-cli -context=genome -manifest=_updated_manifest.manifest +INFO : Submission(s) validated successfully +INFO : The submission has been completed successfully +INFO : This was a TEST submission(s) diff --git a/modules/local/ena_webin_cli/test-mocking/mock_validate.report b/modules/local/ena_webin_cli/test-mocking/mock_validate.report new file mode 100644 index 0000000..b3f9e7a --- /dev/null +++ b/modules/local/ena_webin_cli/test-mocking/mock_validate.report @@ -0,0 +1,3 @@ +INFO : MOCK WEBIN RUN +INFO : command=ena-webin-cli -context=genome -manifest=_updated_manifest.manifest +INFO : Submission(s) validated successfully From 4160b5e6d64266804262634c5f1457734dafd146 Mon Sep 17 00:00:00 2001 From: "Juan F. Mosquera" Date: Sat, 4 Apr 2026 14:45:48 +0100 Subject: [PATCH 6/8] ignore nf-test run generated output --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 0eb3ce9..60ad61e 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,6 @@ testing* null/ .idea/ test_data + +# Ignore Nextflow test output files, which may contain sensitive information and are not relevant to the repository. +.nf-test* From 952eb93b33633be60f9a2646d48af5821fec954e Mon Sep 17 00:00:00 2001 From: "Juan F. Mosquera" Date: Sat, 4 Apr 2026 16:00:11 +0100 Subject: [PATCH 7/8] make mocking available using the env variable WEBINCLI_TEST_MOCK --- modules/local/ena_webin_cli/main.nf.test | 44 ++++++++++++++----- modules/local/ena_webin_cli/nextflow.config | 12 ----- .../test-mocking/nextflow.config | 12 +++++ 3 files changed, 44 insertions(+), 24 deletions(-) delete mode 100644 modules/local/ena_webin_cli/nextflow.config create mode 100644 modules/local/ena_webin_cli/test-mocking/nextflow.config diff --git a/modules/local/ena_webin_cli/main.nf.test b/modules/local/ena_webin_cli/main.nf.test index d84dbd4..0569425 100644 --- a/modules/local/ena_webin_cli/main.nf.test +++ b/modules/local/ena_webin_cli/main.nf.test @@ -2,14 +2,22 @@ nextflow_process { name "Test Process ENA_WEBIN_CLI" script "modules/local/ena_webin_cli/main.nf" process "ENA_WEBIN_CLI" - config "./nextflow.config" + + // Set WEBINCLI_TEST_MOCK=true to run against a mocked ena-webin-cli. + def useMocking = (System.getenv('WEBINCLI_TEST_MOCK') ?: 'false').toBoolean() + def launchDir = System.getProperty('user.dir') + def mockConfigPath = "${launchDir}/modules/local/ena_webin_cli/test-mocking/nextflow.config" test("Run validate with no failures") { + if (useMocking) { + options "-c ${mockConfigPath}" + } + when { params { webincli_submit = false - webincli_mock = true + webincli_mock = useMocking } process { """ @@ -29,10 +37,14 @@ nextflow_process { assert process.success assert process.out.upload_status[0][1] == 'success' def report_lines = path(process.out.webin_report[0][1]).readLines() - assert report_lines.any { it.contains("MOCK WEBIN RUN") } - assert report_lines.any { it.contains("-context=genome") } - assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") } - assert report_lines.any { it.contains("-validate") } + // When mocking it validates the parameters are passed correctly, but doesn't actually run the submission, + // so we check for the presence of the parameters in the report. + if (useMocking) { + assert report_lines.any { it.contains("MOCK WEBIN RUN") } + assert report_lines.any { it.contains("-context=genome") } + assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") } + assert report_lines.any { it.contains("-validate") } + } assert report_lines.any { it.contains("Submission(s) validated successfully") } assert snapshot(process.out.versions).match() } @@ -41,6 +53,10 @@ nextflow_process { } test("Run push with no failures") { + if (useMocking) { + options "-c ${mockConfigPath}" + } + setup { run("GENERATE_TEST_DATA") { script "./setup_test.nf" @@ -59,7 +75,7 @@ nextflow_process { params { webincli_submit = true test_upload = true - webincli_mock = true + webincli_mock = useMocking } process { """ @@ -81,11 +97,15 @@ nextflow_process { assert process.success assert process.out.upload_status[0][1] == 'success' def report_lines = path(process.out.webin_report[0][1]).readLines() - assert report_lines.any { it.contains("MOCK WEBIN RUN") } - assert report_lines.any { it.contains("-context=genome") } - assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") } - assert report_lines.any { it.contains("-submit") } - assert report_lines.any { it.contains("-test") } + // When mocking it validates the parameters are passed correctly, but doesn't actually run the submission, + // so we check for the presence of the parameters in the report. + if (useMocking) { + assert report_lines.any { it.contains("MOCK WEBIN RUN") } + assert report_lines.any { it.contains("-context=genome") } + assert report_lines.any { it.contains("-manifest=lachnospira_eligens_updated_manifest.manifest") } + assert report_lines.any { it.contains("-submit") } + assert report_lines.any { it.contains("-test") } + } assert report_lines.any { it.contains("Submission(s) validated successfully") } assert report_lines.any { it.contains("The submission has been completed successfully") } assert report_lines.any { it.contains("This was a TEST submission(s)") } diff --git a/modules/local/ena_webin_cli/nextflow.config b/modules/local/ena_webin_cli/nextflow.config deleted file mode 100644 index 910e90b..0000000 --- a/modules/local/ena_webin_cli/nextflow.config +++ /dev/null @@ -1,12 +0,0 @@ -params.testDataDir = "${projectDir}/modules/local/ena_webin_cli/test-mocking" -env { - WEBIN_ACCOUNT = "mock_account" - WEBIN_PASSWORD = "mock_password" - PATH = "${params.testDataDir}:\$PATH" - WEBINCLI_MOCK_TEMPLATE_DIR = "${params.testDataDir}" -} -process { - withName: 'ENA_WEBIN_CLI' { - containerOptions = "-v ${params.testDataDir}:${params.testDataDir}" - } -} diff --git a/modules/local/ena_webin_cli/test-mocking/nextflow.config b/modules/local/ena_webin_cli/test-mocking/nextflow.config new file mode 100644 index 0000000..b85eebe --- /dev/null +++ b/modules/local/ena_webin_cli/test-mocking/nextflow.config @@ -0,0 +1,12 @@ +params.testMockingDir = "${projectDir}/modules/local/ena_webin_cli/test-mocking" +env { + WEBIN_ACCOUNT = "mock_account" + WEBIN_PASSWORD = "mock_password" + PATH = "${params.testMockingDir}:\$PATH" + WEBINCLI_MOCK_TEMPLATE_DIR = "${params.testMockingDir}" +} +process { + withName: 'ENA_WEBIN_CLI' { + containerOptions = "-v ${params.testMockingDir}:${params.testMockingDir}" + } +} From 46f2a2ba128012fe90d627d935c0e5ddebfec7a5 Mon Sep 17 00:00:00 2001 From: "Juan F. Mosquera" Date: Sat, 4 Apr 2026 16:20:52 +0100 Subject: [PATCH 8/8] pre-commit fix --- modules/local/ena_webin_cli/test-mocking/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/ena_webin_cli/test-mocking/nextflow.config b/modules/local/ena_webin_cli/test-mocking/nextflow.config index b85eebe..07ada48 100644 --- a/modules/local/ena_webin_cli/test-mocking/nextflow.config +++ b/modules/local/ena_webin_cli/test-mocking/nextflow.config @@ -7,6 +7,6 @@ env { } process { withName: 'ENA_WEBIN_CLI' { - containerOptions = "-v ${params.testMockingDir}:${params.testMockingDir}" + containerOptions = "-v ${params.testMockingDir}:${params.testMockingDir}" } }