From 4cf72b43e4d7668e9efbd6784a2ed8afb013bf00 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 16 Aug 2023 18:55:23 +0100 Subject: [PATCH 1/7] Restructure local modules and main script names --- .../{multiqc_mappings_config.nf => main.nf} | 0 .../{multiqc_mappings_config.nf.test => tests/main.nf.test} | 0 .../main.nf.test.snap} | 0 modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf => main.nf} | 0 .../sra_fastq_ftp/{sra_fastq_ftp.nf.test => tests/main.nf.test} | 0 .../{sra_fastq_ftp.nf.test.snap => tests/main.nf.test.snap} | 0 .../local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf => main.nf} | 0 .../{sra_ids_to_runinfo.nf.test => tests/main.nf.test} | 0 .../{sra_ids_to_runinfo.nf.test.snap => tests/main.nf.test.snap} | 0 .../sra_merge_samplesheet/{sra_merge_samplesheet.nf => main.nf} | 0 .../{sra_merge_samplesheet.nf.test => tests/main.nf.test} | 0 .../main.nf.test.snap} | 0 .../local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf => main.nf} | 0 .../{sra_runinfo_to_ftp.nf.test => tests/main.nf.test} | 0 .../{sra_runinfo_to_ftp.nf.test.snap => tests/main.nf.test.snap} | 0 .../local/sra_to_samplesheet/{sra_to_samplesheet.nf => main.nf} | 0 .../{sra_to_samplesheet.nf.test => tests/main.nf.test} | 0 modules/local/synapse_get/{synapse_get.nf => main.nf} | 0 modules/local/synapse_list/{synapse_list.nf => main.nf} | 0 .../{synapse_merge_samplesheet.nf => main.nf} | 0 modules/local/synapse_show/{synapse_show.nf => main.nf} | 0 .../synapse_to_samplesheet.nf => synapse_to_samplesheet/main.nf} | 0 workflows/sra/tests/{sra.nf.test => main.nf.test} | 0 workflows/sra/tests/{sra.nf.test.snap => main.nf.test.snap} | 0 workflows/synapse/tests/{synapse.test => main.nf.test} | 0 25 files changed, 0 insertions(+), 0 deletions(-) rename modules/local/multiqc_mappings_config/{multiqc_mappings_config.nf => main.nf} (100%) rename modules/local/multiqc_mappings_config/{multiqc_mappings_config.nf.test => tests/main.nf.test} (100%) rename modules/local/multiqc_mappings_config/{multiqc_mappings_config.nf.test.snap => tests/main.nf.test.snap} (100%) rename modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf => main.nf} (100%) rename modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf.test => tests/main.nf.test} (100%) rename modules/local/sra_fastq_ftp/{sra_fastq_ftp.nf.test.snap => tests/main.nf.test.snap} (100%) rename modules/local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf => main.nf} (100%) rename modules/local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf.test => tests/main.nf.test} (100%) rename modules/local/sra_ids_to_runinfo/{sra_ids_to_runinfo.nf.test.snap => tests/main.nf.test.snap} (100%) rename modules/local/sra_merge_samplesheet/{sra_merge_samplesheet.nf => main.nf} (100%) rename modules/local/sra_merge_samplesheet/{sra_merge_samplesheet.nf.test => tests/main.nf.test} (100%) rename modules/local/sra_merge_samplesheet/{sra_merge_samplesheet.nf.test.snap => tests/main.nf.test.snap} (100%) rename modules/local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf => main.nf} (100%) rename modules/local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf.test => tests/main.nf.test} (100%) rename modules/local/sra_runinfo_to_ftp/{sra_runinfo_to_ftp.nf.test.snap => tests/main.nf.test.snap} (100%) rename modules/local/sra_to_samplesheet/{sra_to_samplesheet.nf => main.nf} (100%) rename modules/local/sra_to_samplesheet/{sra_to_samplesheet.nf.test => tests/main.nf.test} (100%) rename modules/local/synapse_get/{synapse_get.nf => main.nf} (100%) rename modules/local/synapse_list/{synapse_list.nf => main.nf} (100%) rename modules/local/synapse_merge_samplesheet/{synapse_merge_samplesheet.nf => main.nf} (100%) rename modules/local/synapse_show/{synapse_show.nf => main.nf} (100%) rename modules/local/{synapse_to_sampleshee/synapse_to_samplesheet.nf => synapse_to_samplesheet/main.nf} (100%) rename workflows/sra/tests/{sra.nf.test => main.nf.test} (100%) rename workflows/sra/tests/{sra.nf.test.snap => main.nf.test.snap} (100%) rename workflows/synapse/tests/{synapse.test => main.nf.test} (100%) diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf b/modules/local/multiqc_mappings_config/main.nf similarity index 100% rename from modules/local/multiqc_mappings_config/multiqc_mappings_config.nf rename to modules/local/multiqc_mappings_config/main.nf diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test similarity index 100% rename from modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test rename to modules/local/multiqc_mappings_config/tests/main.nf.test diff --git a/modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap similarity index 100% rename from modules/local/multiqc_mappings_config/multiqc_mappings_config.nf.test.snap rename to modules/local/multiqc_mappings_config/tests/main.nf.test.snap diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf b/modules/local/sra_fastq_ftp/main.nf similarity index 100% rename from modules/local/sra_fastq_ftp/sra_fastq_ftp.nf rename to modules/local/sra_fastq_ftp/main.nf diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test similarity index 100% rename from modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test rename to modules/local/sra_fastq_ftp/tests/main.nf.test diff --git a/modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap similarity index 100% rename from modules/local/sra_fastq_ftp/sra_fastq_ftp.nf.test.snap rename to modules/local/sra_fastq_ftp/tests/main.nf.test.snap diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf b/modules/local/sra_ids_to_runinfo/main.nf similarity index 100% rename from modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf rename to modules/local/sra_ids_to_runinfo/main.nf diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test similarity index 100% rename from modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test rename to modules/local/sra_ids_to_runinfo/tests/main.nf.test diff --git a/modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap similarity index 100% rename from modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf.test.snap rename to modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf b/modules/local/sra_merge_samplesheet/main.nf similarity index 100% rename from modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf rename to modules/local/sra_merge_samplesheet/main.nf diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test similarity index 100% rename from modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test rename to modules/local/sra_merge_samplesheet/tests/main.nf.test diff --git a/modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap similarity index 100% rename from modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf.test.snap rename to modules/local/sra_merge_samplesheet/tests/main.nf.test.snap diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf b/modules/local/sra_runinfo_to_ftp/main.nf similarity index 100% rename from modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf rename to modules/local/sra_runinfo_to_ftp/main.nf diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test similarity index 100% rename from modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test rename to modules/local/sra_runinfo_to_ftp/tests/main.nf.test diff --git a/modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap similarity index 100% rename from modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf.test.snap rename to modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf b/modules/local/sra_to_samplesheet/main.nf similarity index 100% rename from modules/local/sra_to_samplesheet/sra_to_samplesheet.nf rename to modules/local/sra_to_samplesheet/main.nf diff --git a/modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test similarity index 100% rename from modules/local/sra_to_samplesheet/sra_to_samplesheet.nf.test rename to modules/local/sra_to_samplesheet/tests/main.nf.test diff --git a/modules/local/synapse_get/synapse_get.nf b/modules/local/synapse_get/main.nf similarity index 100% rename from modules/local/synapse_get/synapse_get.nf rename to modules/local/synapse_get/main.nf diff --git a/modules/local/synapse_list/synapse_list.nf b/modules/local/synapse_list/main.nf similarity index 100% rename from modules/local/synapse_list/synapse_list.nf rename to modules/local/synapse_list/main.nf diff --git a/modules/local/synapse_merge_samplesheet/synapse_merge_samplesheet.nf b/modules/local/synapse_merge_samplesheet/main.nf similarity index 100% rename from modules/local/synapse_merge_samplesheet/synapse_merge_samplesheet.nf rename to modules/local/synapse_merge_samplesheet/main.nf diff --git a/modules/local/synapse_show/synapse_show.nf b/modules/local/synapse_show/main.nf similarity index 100% rename from modules/local/synapse_show/synapse_show.nf rename to modules/local/synapse_show/main.nf diff --git a/modules/local/synapse_to_sampleshee/synapse_to_samplesheet.nf b/modules/local/synapse_to_samplesheet/main.nf similarity index 100% rename from modules/local/synapse_to_sampleshee/synapse_to_samplesheet.nf rename to modules/local/synapse_to_samplesheet/main.nf diff --git a/workflows/sra/tests/sra.nf.test b/workflows/sra/tests/main.nf.test similarity index 100% rename from workflows/sra/tests/sra.nf.test rename to workflows/sra/tests/main.nf.test diff --git a/workflows/sra/tests/sra.nf.test.snap b/workflows/sra/tests/main.nf.test.snap similarity index 100% rename from workflows/sra/tests/sra.nf.test.snap rename to workflows/sra/tests/main.nf.test.snap diff --git a/workflows/synapse/tests/synapse.test b/workflows/synapse/tests/main.nf.test similarity index 100% rename from workflows/synapse/tests/synapse.test rename to workflows/synapse/tests/main.nf.test From 168a6812bf84e1044520b2907b79c987ba2bb892 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 17 Aug 2023 11:31:36 +0100 Subject: [PATCH 2/7] Fix tests and standardise tags --- main.nf | 4 ++-- .../multiqc_mappings_config/tests/main.nf.test | 5 +++-- modules/local/sra_fastq_ftp/tests/main.nf.test | 5 +++-- .../local/sra_ids_to_runinfo/tests/main.nf.test | 5 +++-- .../sra_merge_samplesheet/tests/main.nf.test | 5 +++-- .../local/sra_runinfo_to_ftp/tests/main.nf.test | 5 +++-- .../local/sra_to_samplesheet/tests/main.nf.test | 4 +++- workflows/sra/main.nf | 16 ++++++++-------- workflows/sra/tests/main.nf.test | 3 ++- workflows/sra/tests/skip_fastq.nf.test | 3 ++- .../sra/tests/with_atacseq_samplesheet.nf.test | 3 ++- .../sra/tests/with_rnaseq_samplesheet.nf.test | 3 ++- .../with_rnaseq_specific_ena_metadata.nf.test | 3 ++- workflows/sra/tests/with_sratools.nf.test | 3 ++- .../tests/with_taxprofiler_samplesheet.nf.test | 3 ++- .../tests/with_viralrecon_samplesheet.nf.test | 3 ++- workflows/synapse/main.nf | 2 +- workflows/synapse/tests/main.nf.test | 4 +++- 18 files changed, 48 insertions(+), 31 deletions(-) diff --git a/main.nf b/main.nf index f856a93c..6da732be 100644 --- a/main.nf +++ b/main.nf @@ -49,9 +49,9 @@ if (WorkflowMain.isSraId(ch_input)) { if (params.input_type == input_type) { if (params.input_type == 'sra') { - include { SRA } from './workflows/sra/main' + include { SRA } from './workflows/sra' } else if (params.input_type == 'synapse') { - include { SYNAPSE } from './workflows/synapse/main' + include { SYNAPSE } from './workflows/synapse' } } else { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index a5c148dc..26dbe22f 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -1,10 +1,11 @@ nextflow_process { name "Test Process MULTIQC_MAPPINGS_CONFIG" - script "modules/local/multiqc_mappings_config/multiqc_mappings_config.nf" + script "modules/local/multiqc_mappings_config/main.nf" process "MULTIQC_MAPPINGS_CONFIG" - tag "multiqc_mappings_config" + tag "modules" tag "modules_local" + tag "multiqc_mappings_config" test("SRX9626017_SRR13191702") { diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index 5fa043ab..e8b0d406 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -1,10 +1,11 @@ nextflow_process { name "Test Process SRA_FASTQ_FTP" - script "modules/local/sra_fastq_ftp/sra_fastq_ftp.nf" + script "modules/local/sra_fastq_ftp/main.nf" process "SRA_FASTQ_FTP" - tag "sra_fastq_ftp" + tag "modules" tag "modules_local" + tag "sra_fastq_ftp" test("SRX9626017_SRR13191702") { diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test index a89e21fa..a140efdc 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -1,10 +1,11 @@ nextflow_process { name "Test Process SRA_IDS_TO_RUNINFO" - script "modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo.nf" + script "modules/local/sra_ids_to_runinfo/main.nf" process "SRA_IDS_TO_RUNINFO" - tag "sra_ids_to_runinfo" + tag "modules" tag "modules_local" + tag "sra_ids_to_runinfo" test("Should run without failures") { diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test index 9385dab8..6ff471e8 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -1,10 +1,11 @@ nextflow_process { name "Test Process SRA_MERGE_SAMPLESHEET" - script "modules/local/sra_merge_samplesheet/sra_merge_samplesheet.nf" + script "modules/local/sra_merge_samplesheet/main.nf" process "SRA_MERGE_SAMPLESHEET" - tag "sra_merge_samplesheet" + tag "modules" tag "modules_local" + tag "sra_merge_samplesheet" test("Should run without failures") { diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test index dfff36fe..154ae4eb 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -1,10 +1,11 @@ nextflow_process { name "Test Process SRA_RUNINFO_TO_FTP" - script "modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp.nf" + script "modules/local/sra_runinfo_to_ftp/main.nf" process "SRA_RUNINFO_TO_FTP" - tag "sra_runinfo_to_ftp" + tag "modules" tag "modules_local" + tag "sra_runinfo_to_ftp" test("Should run without failures") { diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index 5c7ff7d9..7448fe1d 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -1,8 +1,10 @@ nextflow_process { name "Test Process SRA_TO_SAMPLESHEET" - script "modules/local/sra_to_samplesheet/sra_to_samplesheet.nf" + script "modules/local/sra_to_samplesheet/main.nf" process "SRA_TO_SAMPLESHEET" + tag "modules" + tag "modules_local" tag "sra_to_samplesheet" test("Should run without failures") { diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 05b9a80d..512a73d4 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -19,12 +19,12 @@ WorkflowSra.initialise(params, valid_params) ======================================================================================== */ -include { SRA_IDS_TO_RUNINFO } from '../../modules/local/sra_ids_to_runinfo/sra_ids_to_runinfo' -include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp/sra_runinfo_to_ftp' -include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp/sra_fastq_ftp' -include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet/sra_to_samplesheet' -include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet/sra_merge_samplesheet' -include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config/multiqc_mappings_config' +include { SRA_IDS_TO_RUNINFO } from '../../modules/local/sra_ids_to_runinfo' +include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp' +include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' +include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' +include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' +include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' /* ======================================================================================== @@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' -include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main' +include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools' /* ======================================================================================== diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 16074b64..4fa13985 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" tag "sra" - tag "workflow" + tag "sra_default" test("SRA FASTQ & Metadata") { diff --git a/workflows/sra/tests/skip_fastq.nf.test b/workflows/sra/tests/skip_fastq.nf.test index 38814a77..188f0652 100644 --- a/workflows/sra/tests/skip_fastq.nf.test +++ b/workflows/sra/tests/skip_fastq.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_skip_fastq" - tag "workflow" test("SRA Skip FASTQ") { diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test b/workflows/sra/tests/with_atacseq_samplesheet.nf.test index 4ebc9352..13f41868 100644 --- a/workflows/sra/tests/with_atacseq_samplesheet.nf.test +++ b/workflows/sra/tests/with_atacseq_samplesheet.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_with_atacseq" - tag "workflow" test("SRA NF-CORE/ATACSEQ Samplesheet") { diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test index ca77778c..fce8853c 100644 --- a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test +++ b/workflows/sra/tests/with_rnaseq_samplesheet.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_with_rnaseq" - tag "workflow" test("SRA NF-CORE/RNASEQ Samplesheet") { diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test index 2fc12241..b9956366 100644 --- a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test +++ b/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_with_rnaseq_specific_ena" - tag "workflow" test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") { diff --git a/workflows/sra/tests/with_sratools.nf.test b/workflows/sra/tests/with_sratools.nf.test index 839e3089..e3239a18 100644 --- a/workflows/sra/tests/with_sratools.nf.test +++ b/workflows/sra/tests/with_sratools.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_force_sratools_download" - tag "workflow" test("Force SRA-Tools Download") { diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test index 7ffbca59..9d6e5f1f 100644 --- a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test +++ b/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_with_taxprofiler" - tag "workflow" test("SRA NF-CORE/TAXPROFILER Samplesheet") { diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test index e10e2db8..429a114a 100644 --- a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test +++ b/workflows/sra/tests/with_viralrecon_samplesheet.nf.test @@ -2,8 +2,9 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "sra" tag "sra_with_viralrecon" - tag "workflow" test("SRA NF-CORE/VIRALRECON Samplesheet") { diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 7d871659..f8cbeba1 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' /* ======================================================================================== diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test index 464ad226..efb7d793 100644 --- a/workflows/synapse/tests/main.nf.test +++ b/workflows/synapse/tests/main.nf.test @@ -2,8 +2,10 @@ nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "workflows" + tag "synapse" + tag "synapse_default" profile "test_synapse" - tag "pipeline" test("Synapse Input Type") { From 53f75ecc1e9e8e7ea57fce3d494c282f45edd90d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 17 Aug 2023 11:31:55 +0100 Subject: [PATCH 3/7] Use generic tags in CI tests --- .github/workflows/ci.yml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0abe1037..5f329342 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,15 +44,8 @@ jobs: matrix: NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} test_tags: - - "sra" - - "sra_force_sratools_download" - - "sra_skip_fastq" - - "sra_with_atacseq" - - "sra_with_rnaseq" - - "sra_with_rnaseq_specific_ena" - - "sra_with_taxprofiler" - - "sra_with_viralrecon" - "modules_local" + - "sra" profile: - "docker" From e49ad85996f27286b1e0971063bbb1f7e683af42 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 17 Aug 2023 12:51:05 +0100 Subject: [PATCH 4/7] Fix tests for sra_to_samplesheet module --- .../tests/main.nf.test.snap | 113 ++++++++++++++++++ 1 file changed, 113 insertions(+) create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap new file mode 100644 index 00000000..8b5f4947 --- /dev/null +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -0,0 +1,113 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", + "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" + ] + ], + "1": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", + "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" + ] + ], + "mappings": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", + "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" + ] + ], + "samplesheet": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", + "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" + ] + ] + } + ], + "timestamp": "2023-08-17T10:55:52+0000" + } +} \ No newline at end of file From 885ba0f30cc0c6925b081d14eb2720e6299e9136 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 17 Aug 2023 12:51:32 +0100 Subject: [PATCH 5/7] Rename workflows and standardise tags --- .github/workflows/ci.yml | 9 ++++- .../tests/main.nf.test | 9 ++--- .../local/sra_fastq_ftp/tests/main.nf.test | 15 ++++---- .../sra_ids_to_runinfo/tests/main.nf.test | 7 ++-- .../sra_merge_samplesheet/tests/main.nf.test | 7 ++-- .../sra_runinfo_to_ftp/tests/main.nf.test | 7 ++-- .../sra_to_samplesheet/tests/main.nf.test | 13 +++---- workflows/sra/tests/main.nf.test | 38 ++++++++++--------- ...=> sra_custom_ena_metadata_fields.nf.test} | 14 +++---- ...a_custom_ena_metadata_fields.nf.test.snap} | 0 ...st => sra_force_sratools_download.nf.test} | 10 ++--- ... sra_force_sratools_download.nf.test.snap} | 0 ...t => sra_nf_core_pipeline_atacseq.nf.test} | 10 ++--- ...sra_nf_core_pipeline_atacseq.nf.test.snap} | 0 ...st => sra_nf_core_pipeline_rnaseq.nf.test} | 10 ++--- ... sra_nf_core_pipeline_rnaseq.nf.test.snap} | 0 ... sra_nf_core_pipeline_taxprofiler.nf.test} | 11 +++--- ...nf_core_pipeline_taxprofiler.nf.test.snap} | 0 ...> sra_nf_core_pipeline_viralrecon.nf.test} | 10 ++--- ..._nf_core_pipeline_viralrecon.nf.test.snap} | 0 ...f.test => sra_skip_fastq_download.nf.test} | 12 +++--- ...p => sra_skip_fastq_download.nf.test.snap} | 0 workflows/synapse/tests/main.nf.test | 2 +- 23 files changed, 91 insertions(+), 93 deletions(-) rename workflows/sra/tests/{with_rnaseq_specific_ena_metadata.nf.test => sra_custom_ena_metadata_fields.nf.test} (81%) rename workflows/sra/tests/{with_rnaseq_specific_ena_metadata.nf.test.snap => sra_custom_ena_metadata_fields.nf.test.snap} (100%) rename workflows/sra/tests/{with_sratools.nf.test => sra_force_sratools_download.nf.test} (92%) rename workflows/sra/tests/{with_sratools.nf.test.snap => sra_force_sratools_download.nf.test.snap} (100%) rename workflows/sra/tests/{with_atacseq_samplesheet.nf.test => sra_nf_core_pipeline_atacseq.nf.test} (90%) rename workflows/sra/tests/{with_atacseq_samplesheet.nf.test.snap => sra_nf_core_pipeline_atacseq.nf.test.snap} (100%) rename workflows/sra/tests/{with_rnaseq_samplesheet.nf.test => sra_nf_core_pipeline_rnaseq.nf.test} (90%) rename workflows/sra/tests/{with_rnaseq_samplesheet.nf.test.snap => sra_nf_core_pipeline_rnaseq.nf.test.snap} (100%) rename workflows/sra/tests/{with_taxprofiler_samplesheet.nf.test => sra_nf_core_pipeline_taxprofiler.nf.test} (89%) rename workflows/sra/tests/{with_taxprofiler_samplesheet.nf.test.snap => sra_nf_core_pipeline_taxprofiler.nf.test.snap} (100%) rename workflows/sra/tests/{with_viralrecon_samplesheet.nf.test => sra_nf_core_pipeline_viralrecon.nf.test} (90%) rename workflows/sra/tests/{with_viralrecon_samplesheet.nf.test.snap => sra_nf_core_pipeline_viralrecon.nf.test.snap} (100%) rename workflows/sra/tests/{skip_fastq.nf.test => sra_skip_fastq_download.nf.test} (94%) rename workflows/sra/tests/{skip_fastq.nf.test.snap => sra_skip_fastq_download.nf.test.snap} (100%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5f329342..451613fb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,7 +45,14 @@ jobs: NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} test_tags: - "modules_local" - - "sra" + - "sra_default_parameters" + - "sra_custom_ena_metadata_fields" + - "sra_force_sratools_download" + - "sra_nf_core_pipeline_atacseq" + - "sra_nf_core_pipeline_rnaseq" + - "sra_nf_core_pipeline_taxprofiler" + - "sra_nf_core_pipeline_viralrecon" + - "sra_skip_fastq_download" profile: - "docker" diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index 26dbe22f..5f08ceca 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -1,18 +1,19 @@ nextflow_process { - name "Test Process MULTIQC_MAPPINGS_CONFIG" + name "Test process: MULTIQC_MAPPINGS_CONFIG" script "modules/local/multiqc_mappings_config/main.nf" process "MULTIQC_MAPPINGS_CONFIG" tag "modules" tag "modules_local" tag "multiqc_mappings_config" - test("SRX9626017_SRR13191702") { + test("Should run without failures") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } + process { """ input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true) @@ -26,7 +27,5 @@ nextflow_process { { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index e8b0d406..33b9b185 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -1,24 +1,25 @@ nextflow_process { - name "Test Process SRA_FASTQ_FTP" + name "Test process: SRA_FASTQ_FTP" script "modules/local/sra_fastq_ftp/main.nf" process "SRA_FASTQ_FTP" tag "modules" tag "modules_local" tag "sra_fastq_ftp" - test("SRX9626017_SRR13191702") { + test("Should run without failures") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } + process { """ input[0] = [ - [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map - params.test_data['modules_local']['sra_fastq_ftp'] - ] + [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map + params.test_data['modules_local']['sra_fastq_ftp'] + ] """ } } @@ -29,7 +30,5 @@ nextflow_process { { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test index a140efdc..3953f008 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -1,6 +1,6 @@ nextflow_process { - name "Test Process SRA_IDS_TO_RUNINFO" + name "Test process: SRA_IDS_TO_RUNINFO" script "modules/local/sra_ids_to_runinfo/main.nf" process "SRA_IDS_TO_RUNINFO" tag "modules" @@ -11,8 +11,9 @@ nextflow_process { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } + process { """ input[0] = 'SRR13191702' @@ -27,7 +28,5 @@ nextflow_process { { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test index 6ff471e8..6012103e 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -1,6 +1,6 @@ nextflow_process { - name "Test Process SRA_MERGE_SAMPLESHEET" + name "Test process: SRA_MERGE_SAMPLESHEET" script "modules/local/sra_merge_samplesheet/main.nf" process "SRA_MERGE_SAMPLESHEET" tag "modules" @@ -11,8 +11,9 @@ nextflow_process { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } + process { """ input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) } @@ -27,7 +28,5 @@ nextflow_process { { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test index 154ae4eb..7311f847 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -1,6 +1,6 @@ nextflow_process { - name "Test Process SRA_RUNINFO_TO_FTP" + name "Test process: SRA_RUNINFO_TO_FTP" script "modules/local/sra_runinfo_to_ftp/main.nf" process "SRA_RUNINFO_TO_FTP" tag "modules" @@ -11,8 +11,9 @@ nextflow_process { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } + process { """ input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true) @@ -26,7 +27,5 @@ nextflow_process { { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index 7448fe1d..163312c7 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -1,6 +1,6 @@ nextflow_process { - name "Test Process SRA_TO_SAMPLESHEET" + name "Test process: SRA_TO_SAMPLESHEET" script "modules/local/sra_to_samplesheet/main.nf" process "SRA_TO_SAMPLESHEET" tag "modules" @@ -11,14 +11,15 @@ nextflow_process { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } + process { """ - input[0] = 'meta' + input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867', experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7', sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false] input[1] = 'rnaseq' - input[2] = 'strandedness' - input[3] = 'mapping_fields' + input[2] = 'auto' + input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' """ } } @@ -29,7 +30,5 @@ nextflow_process { { assert snapshot(process.out).match() }, ) } - } - } diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 4fa13985..0d6aa1a1 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -1,12 +1,12 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_default" + tag "workflows_sra" + tag "sra_default_parameters" - test("SRA FASTQ & Metadata") { + test("Parameters: default") { when { params { @@ -19,23 +19,25 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, + { assert snapshot( + path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), + path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), + path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), + path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), + path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), + path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), + path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), + path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), + path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), + path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") + }, { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, + { assert snapshot( + path("$outputDir/samplesheet/id_mappings.csv"), + path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") + }, { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } ) } - } - } diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test similarity index 81% rename from workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test rename to workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index b9956366..173b9fbd 100644 --- a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -1,18 +1,18 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_with_rnaseq_specific_ena" + tag "workflows_sra" + tag "sra_custom_ena_metadata_fields" - test("SRA NF-CORE/RNASEQ Samplesheet With Specific ENA metadata") { + test("Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'") { when { params { - outdir = "$outputDir" - nf_core_pipeline = "rnaseq" - ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" + outdir = "$outputDir" + nf_core_pipeline = "rnaseq" + ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" sample_mapping_fields = "run_accession,library_layout" } } diff --git a/workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap similarity index 100% rename from workflows/sra/tests/with_rnaseq_specific_ena_metadata.nf.test.snap rename to workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap diff --git a/workflows/sra/tests/with_sratools.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test similarity index 92% rename from workflows/sra/tests/with_sratools.nf.test rename to workflows/sra/tests/sra_force_sratools_download.nf.test index e3239a18..a5c6afa6 100644 --- a/workflows/sra/tests/with_sratools.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -1,16 +1,16 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" + tag "workflows_sra" tag "sra_force_sratools_download" - test("Force SRA-Tools Download") { + test("Parameters: '--force_sratools_download'") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" force_sratools_download = true } } @@ -36,7 +36,5 @@ nextflow_pipeline { { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } ) } - } - } diff --git a/workflows/sra/tests/with_sratools.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap similarity index 100% rename from workflows/sra/tests/with_sratools.nf.test.snap rename to workflows/sra/tests/sra_force_sratools_download.nf.test.snap diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test similarity index 90% rename from workflows/sra/tests/with_atacseq_samplesheet.nf.test rename to workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 13f41868..4286327f 100644 --- a/workflows/sra/tests/with_atacseq_samplesheet.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -1,16 +1,16 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_with_atacseq" + tag "workflows_sra" + tag "sra_nf_core_pipeline_atacseq" - test("SRA NF-CORE/ATACSEQ Samplesheet") { + test("Parameters: '--nf_core_pipeline atacseq'") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" nf_core_pipeline = "atacseq" } } diff --git a/workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap similarity index 100% rename from workflows/sra/tests/with_atacseq_samplesheet.nf.test.snap rename to workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test similarity index 90% rename from workflows/sra/tests/with_rnaseq_samplesheet.nf.test rename to workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index fce8853c..c948e7dc 100644 --- a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -1,16 +1,16 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_with_rnaseq" + tag "workflows_sra" + tag "sra_nf_core_pipeline_rnaseq" - test("SRA NF-CORE/RNASEQ Samplesheet") { + test("Parameters: '--nf_core_pipeline rnaseq'") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" nf_core_pipeline = "rnaseq" } } diff --git a/workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap similarity index 100% rename from workflows/sra/tests/with_rnaseq_samplesheet.nf.test.snap rename to workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test similarity index 89% rename from workflows/sra/tests/with_taxprofiler_samplesheet.nf.test rename to workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index 9d6e5f1f..ab39f52f 100644 --- a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -1,16 +1,16 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_with_taxprofiler" + tag "workflows_sra" + tag "sra_nf_core_pipeline_taxprofiler" - test("SRA NF-CORE/TAXPROFILER Samplesheet") { + test("Parameters: '--nf_core_pipeline taxprofiler'") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" nf_core_pipeline = "taxprofiler" } } @@ -37,5 +37,4 @@ nextflow_pipeline { ) } } - } diff --git a/workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap similarity index 100% rename from workflows/sra/tests/with_taxprofiler_samplesheet.nf.test.snap rename to workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test similarity index 90% rename from workflows/sra/tests/with_viralrecon_samplesheet.nf.test rename to workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 429a114a..c80a092a 100644 --- a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -1,16 +1,16 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_with_viralrecon" + tag "workflows_sra" + tag "sra_nf_core_pipeline_viralrecon" - test("SRA NF-CORE/VIRALRECON Samplesheet") { + test("Parameters: '--nf_core_pipeline viralrecon'") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" nf_core_pipeline = "viralrecon" } } diff --git a/workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap similarity index 100% rename from workflows/sra/tests/with_viralrecon_samplesheet.nf.test.snap rename to workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap diff --git a/workflows/sra/tests/skip_fastq.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test similarity index 94% rename from workflows/sra/tests/skip_fastq.nf.test rename to workflows/sra/tests/sra_skip_fastq_download.nf.test index 188f0652..9a274731 100644 --- a/workflows/sra/tests/skip_fastq.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -1,16 +1,16 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: sra.nf" script "main.nf" tag "workflows" - tag "sra" - tag "sra_skip_fastq" + tag "workflows_sra" + tag "sra_skip_fastq_download" - test("SRA Skip FASTQ") { + test("Parameters: '--skip_fastq_download'") { when { params { - outdir = "$outputDir" + outdir = "$outputDir" skip_fastq_download = true } } @@ -49,7 +49,5 @@ nextflow_pipeline { { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() } ) } - } - } diff --git a/workflows/sra/tests/skip_fastq.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap similarity index 100% rename from workflows/sra/tests/skip_fastq.nf.test.snap rename to workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test index efb7d793..7cbfed11 100644 --- a/workflows/synapse/tests/main.nf.test +++ b/workflows/synapse/tests/main.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf" + name "Test workflow: synapse.nf" script "main.nf" tag "workflows" tag "synapse" From 73ea3ca585f027ae73bd9003f0f5480389ab5528 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 17 Aug 2023 13:06:34 +0100 Subject: [PATCH 6/7] Patch custom/dumpsoftwareversions module to remove NF version dump --- modules.json | 3 ++- .../custom-dumpsoftwareversions.diff | 13 +++++++++++++ .../templates/dumpsoftwareversions.py | 1 - 3 files changed, 15 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff diff --git a/modules.json b/modules.json index 3137b88b..2244addd 100644 --- a/modules.json +++ b/modules.json @@ -8,7 +8,8 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff" }, "custom/sratoolsncbisettings": { "branch": "master", diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff new file mode 100644 index 00000000..a7893b24 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff @@ -0,0 +1,13 @@ +Changes in module 'nf-core/custom/dumpsoftwareversions' +--- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py ++++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +@@ -75,7 +75,6 @@ + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { +- "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + +************************************************************ diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index da033408..33d127f8 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -75,7 +75,6 @@ def main(): versions_by_module[module] = process_versions versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", "$workflow.manifest.name": "$workflow.manifest.version", } From de464567cb187f5eddecaa9b0e3c5f8ef3bedd69 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 17 Aug 2023 13:27:34 +0100 Subject: [PATCH 7/7] Use default snapshot for all workflows --- .../tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 27 +++++++++++++++- .../local/sra_fastq_ftp/tests/main.nf.test | 2 +- .../sra_ids_to_runinfo/tests/main.nf.test | 2 +- .../sra_merge_samplesheet/tests/main.nf.test | 2 +- .../sra_runinfo_to_ftp/tests/main.nf.test | 2 +- .../sra_to_samplesheet/tests/main.nf.test | 2 +- workflows/sra/tests/main.nf.test | 21 +----------- workflows/sra/tests/main.nf.test.snap | 16 +++++++--- .../sra_custom_ena_metadata_fields.nf.test | 19 ++--------- ...ra_custom_ena_metadata_fields.nf.test.snap | 16 +++++++--- .../tests/sra_force_sratools_download.nf.test | 19 ++--------- .../sra_force_sratools_download.nf.test.snap | 16 +++++++--- .../sra_nf_core_pipeline_atacseq.nf.test | 19 ++--------- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 16 +++++++--- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 19 ++--------- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 16 +++++++--- .../sra_nf_core_pipeline_taxprofiler.nf.test | 19 ++--------- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 16 +++++++--- .../sra_nf_core_pipeline_viralrecon.nf.test | 19 ++--------- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 16 +++++++--- .../sra/tests/sra_skip_fastq_download.nf.test | 32 ++----------------- .../sra_skip_fastq_download.nf.test.snap | 22 +++++++++++-- 23 files changed, 150 insertions(+), 190 deletions(-) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test index 5f08ceca..3bf79537 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap index e8914aea..9cf7fb38 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -22,6 +22,31 @@ ] } ], - "timestamp": "2023-07-05T15:01:18+0000" + "timestamp": "2023-08-17T12:02:35+0000" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ], + "1": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "versions": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "yml": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ] + } + ], + "timestamp": "2023-08-17T12:02:35+0000" } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test index 33b9b185..7892d156 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test index 3953f008..f8a44086 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -25,7 +25,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test index 6012103e..e37039bd 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -25,7 +25,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test index 7311f847..1558ff39 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test index 163312c7..b2ec5b11 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 0d6aa1a1..39a5cc3f 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -17,26 +17,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot( - path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") - }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot( - path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") - }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index dcdb43b5..88ea9654 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -1,4 +1,12 @@ { + "Parameters: default": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:09:45+0000" + }, "metadata": { "content": [ "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", @@ -12,20 +20,20 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:48:50+0000" + "timestamp": "2023-08-17T12:09:45+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:48:50+0000" + "timestamp": "2023-08-17T12:09:45+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:48:50+0000" + "timestamp": "2023-08-17T12:09:45+0000" }, "fastq": { "content": [ @@ -75,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-06T23:48:50+0000" + "timestamp": "2023-08-17T12:09:45+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 173b9fbd..6e27c4a9 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_custom_ena_metadata_fields" - test("Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'") { + test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { when { params { @@ -20,22 +20,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index bfa3c9cd..55c39d4f 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -12,20 +12,28 @@ "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1", "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236" ], - "timestamp": "2023-07-03T23:38:27+0000" + "timestamp": "2023-08-17T12:11:42+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f", "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040" ], - "timestamp": "2023-07-03T23:38:27+0000" + "timestamp": "2023-08-17T12:11:42+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-07-03T23:38:27+0000" + "timestamp": "2023-08-17T12:11:42+0000" + }, + "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:11:42+0000" }, "fastq": { "content": [ @@ -75,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-07-03T23:38:27+0000" + "timestamp": "2023-08-17T12:11:42+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index a5c6afa6..1b501975 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_force_sratools_download" - test("Parameters: '--force_sratools_download'") { + test("Parameters: --force_sratools_download") { when { params { @@ -18,22 +18,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index bbec9969..d5d694da 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -1,4 +1,12 @@ { + "Parameters: '--force_sratools_download'": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:15:55+0000" + }, "metadata": { "content": [ "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", @@ -12,20 +20,20 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:43:45+0000" + "timestamp": "2023-08-17T12:15:55+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:43:45+0000" + "timestamp": "2023-08-17T12:15:55+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:43:45+0000" + "timestamp": "2023-08-17T12:15:55+0000" }, "fastq": { "content": [ @@ -54,6 +62,6 @@ "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7", "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af" ], - "timestamp": "2023-08-06T23:43:45+0000" + "timestamp": "2023-08-17T12:15:55+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 4286327f..bda1d724 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_nf_core_pipeline_atacseq" - test("Parameters: '--nf_core_pipeline atacseq'") { + test("Parameters: --nf_core_pipeline atacseq") { when { params { @@ -18,22 +18,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index a9dd40a0..c99f258e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -12,20 +12,28 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:38:47+0000" + "timestamp": "2023-08-17T12:21:36+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:38:47+0000" + "timestamp": "2023-08-17T12:21:36+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:38:47+0000" + "timestamp": "2023-08-17T12:21:36+0000" + }, + "Parameters: '--nf_core_pipeline atacseq'": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:21:36+0000" }, "fastq": { "content": [ @@ -75,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-06T23:38:47+0000" + "timestamp": "2023-08-17T12:21:36+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index c948e7dc..438b7f55 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_nf_core_pipeline_rnaseq" - test("Parameters: '--nf_core_pipeline rnaseq'") { + test("Parameters: --nf_core_pipeline rnaseq") { when { params { @@ -18,22 +18,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 1e3e8a5b..1da0381a 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -12,20 +12,28 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:50:46+0000" + "timestamp": "2023-08-17T12:19:51+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:50:46+0000" + "timestamp": "2023-08-17T12:19:51+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:50:46+0000" + "timestamp": "2023-08-17T12:19:51+0000" + }, + "Parameters: '--nf_core_pipeline rnaseq'": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:19:51+0000" }, "fastq": { "content": [ @@ -75,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-06T23:50:46+0000" + "timestamp": "2023-08-17T12:19:51+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index ab39f52f..301938c4 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_nf_core_pipeline_taxprofiler" - test("Parameters: '--nf_core_pipeline taxprofiler'") { + test("Parameters: --nf_core_pipeline taxprofiler") { when { params { @@ -18,22 +18,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index b4fe3748..85f3957b 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -12,20 +12,28 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:40:33+0000" + "timestamp": "2023-08-17T12:24:34+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:40:33+0000" + "timestamp": "2023-08-17T12:24:34+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:40:33+0000" + "timestamp": "2023-08-17T12:24:34+0000" + }, + "Parameters: --nf_core_pipeline taxprofiler": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:24:34+0000" }, "fastq": { "content": [ @@ -75,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-06T23:40:33+0000" + "timestamp": "2023-08-17T12:24:34+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index c80a092a..892a7c3a 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_nf_core_pipeline_viralrecon" - test("Parameters: '--nf_core_pipeline viralrecon'") { + test("Parameters: --nf_core_pipeline viralrecon") { when { params { @@ -18,22 +18,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/fastq/").list()).match("fastq") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 51b0ea51..13c59b5d 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -12,20 +12,28 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:34:45+0000" + "timestamp": "2023-08-17T12:26:57+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:34:45+0000" + "timestamp": "2023-08-17T12:26:57+0000" + }, + "Parameters: --nf_core_pipeline viralrecon": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:26:57+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:34:45+0000" + "timestamp": "2023-08-17T12:26:57+0000" }, "fastq": { "content": [ @@ -75,6 +83,6 @@ "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" ] ], - "timestamp": "2023-08-06T23:34:45+0000" + "timestamp": "2023-08-17T12:26:57+0000" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 9a274731..7d218cf7 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "workflows_sra" tag "sra_skip_fastq_download" - test("Parameters: '--skip_fastq_download'") { + test("Parameters: --skip_fastq_download") { when { params { @@ -18,35 +18,7 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(NftestUtils.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/metadata/DRR026872.runinfo_ftp.tsv"), - path("$outputDir/metadata/DRR028935.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1109373.runinfo_ftp.tsv"), - path("$outputDir/metadata/ERR1160846.runinfo_ftp.tsv"), - path("$outputDir/metadata/GSE214215.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR12848126.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR13191702.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14593545.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR14709033.runinfo_ftp.tsv"), - path("$outputDir/metadata/SRR9984183.runinfo_ftp.tsv")).match("metadata") }, - { assert new File("$outputDir/metadata/GSM4907283.runinfo_ftp.tsv").exists() }, - { assert snapshot(path("$outputDir/samplesheet/id_mappings.csv"), - path("$outputDir/samplesheet/multiqc_config.yml")).match("samplesheet") }, - { assert new File("$outputDir/samplesheet/samplesheet.csv").exists() }, - { assert !new File("$outputDir/fastq/DRX024467_DRR026872.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/ERX1188904_ERR1109373_1.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/ERX1188904_ERR1109373_2.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX10940790_SRR14593545_2.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX11047067_SRR14709033.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX6725035_SRR9984183.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX9315476_SRR12848126_1.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX9315476_SRR12848126_2.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_1.fastq.gz").exists() }, - { assert !new File("$outputDir/fastq/SRX9626017_SRR13191702_2.fastq.gz").exists() } + { assert snapshot(process.out).match() } ) } } diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 7f71a838..d004d5d2 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -1,4 +1,12 @@ { + "Parameters: '--skip_fastq_download'": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:25:19+0000" + }, "metadata": { "content": [ "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", @@ -12,19 +20,27 @@ "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" ], - "timestamp": "2023-08-06T23:37:00+0000" + "timestamp": "2023-08-17T12:25:19+0000" }, "samplesheet": { "content": [ "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" ], - "timestamp": "2023-08-06T23:37:00+0000" + "timestamp": "2023-08-17T12:25:19+0000" }, "software_versions": { "content": [ "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" ], - "timestamp": "2023-08-06T23:37:00+0000" + "timestamp": "2023-08-17T12:25:19+0000" + }, + "Parameters: --skip_fastq_download": { + "content": [ + { + + } + ], + "timestamp": "2023-08-17T12:25:19+0000" } } \ No newline at end of file