From 94fe6092cf313e650b7f4bed6b6ad041da20f09c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 10 Dec 2024 13:37:56 +0100 Subject: [PATCH 1/6] remove double nested folder --- CHANGELOG.md | 1 + conf/modules.config | 2 +- modules/local/fusionreport/download/main.nf | 22 ++++++++++----------- 3 files changed, 13 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 690024b2..b7b8659c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504) - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541) - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548) +- Remove double nested folder introduced in [#572](https://github.com/nf-core/rnafusion/pull/577), []() ### Fixed diff --git a/conf/modules.config b/conf/modules.config index abe0e79d..264d1c87 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -114,7 +114,7 @@ process { ext.args = { {params.no_cosmic} ? "--no-cosmic" : " --cosmic_usr ${params.cosmic_username} --cosmic_passwd ${params.cosmic_passwd}" } ext.args2 = { params.qiagen ? "--qiagen" : "" } publishDir = [ - path: { "${params.genomes_base}/fusion_report_db" }, + path: { "${params.genomes_base}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index b19a6446..89f631db 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -6,17 +6,17 @@ process FUSIONREPORT_DOWNLOAD { container "docker.io/clinicalgenomics/fusion-report:3.1.0" output: - tuple val(meta), path("fusionreport_dbs"), emit: fusionreport_db + tuple val(meta), path("fusion_report_db"), emit: fusionreport_ref path "versions.yml" , emit: versions script: - meta = [id: 'fusionreport_dbs'] + meta = [id: 'fusion_report_db'] def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' """ fusion_report download $args ./ - mkdir fusionreport_dbs - mv *.txt *.log *.db fusionreport_dbs + mkdir fusion_report_db + mv *.txt *.log *.db fusion_report_db/ cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -25,14 +25,14 @@ process FUSIONREPORT_DOWNLOAD { """ stub: - meta = [id: 'fusionreport_dbs'] + meta = [id: 'fusion_report_db'] """ - mkdir fusionreport_dbs - touch fusionreport_dbs/cosmic.db - touch fusionreport_dbs/fusiongdb2.db - touch fusionreport_dbs/mitelman.db - touch fusionreport_dbs/DB-timestamp.txt - touch fusionreport_dbs/fusion_report.log + mkdir fusion_report_db + touch fusion_report_db/cosmic.db + touch fusion_report_db/fusiongdb2.db + touch fusion_report_db/mitelman.db + touch fusion_report_db/DB-timestamp.txt + touch fusion_report_db/fusion_report.log cat <<-END_VERSIONS > versions.yml "${task.process}": From e52244904c69d632320322f911c935d396c60fad Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 10 Dec 2024 13:39:19 +0100 Subject: [PATCH 2/6] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b7b8659c..a2603f3e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504) - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541) - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548) -- Remove double nested folder introduced in [#572](https://github.com/nf-core/rnafusion/pull/577), []() +- Remove double nested folder introduced in [#572](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581) ### Fixed From 18ab239ce99002d3bab715c734ce3010b704ec5a Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 10 Dec 2024 13:40:24 +0100 Subject: [PATCH 3/6] update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a2603f3e..0371c206 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560) - Add nf-test to local subworkflow: `QC_WORKFLOW` [#568](https://github.com/nf-core/rnafusion/pull/568) - Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572) -- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#572](https://github.com/nf-core/rnafusion/pull/577) +- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#577](https://github.com/nf-core/rnafusion/pull/577) ### Changed @@ -27,7 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504) - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541) - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548) -- Remove double nested folder introduced in [#572](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581) +- Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581) ### Fixed From 2e928ed27519168d7ee851a9e593496031d5e104 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 10 Dec 2024 14:59:16 +0100 Subject: [PATCH 4/6] update test --- modules/local/fusionreport/detect/tests/main.nf.test | 5 ++--- modules/local/fusionreport/detect/tests/main.nf.test.snap | 6 +++--- modules/local/fusionreport/download/tests/main.nf.test | 8 ++++---- .../local/fusionreport/download/tests/main.nf.test.snap | 8 ++++---- 4 files changed, 13 insertions(+), 14 deletions(-) diff --git a/modules/local/fusionreport/detect/tests/main.nf.test b/modules/local/fusionreport/detect/tests/main.nf.test index bd5ab356..9fc89540 100644 --- a/modules/local/fusionreport/detect/tests/main.nf.test +++ b/modules/local/fusionreport/detect/tests/main.nf.test @@ -33,8 +33,7 @@ nextflow_process { file("https://github.com/Clinical-Genomics/fusion-report/raw/master/tests/test_data/fusioncatcher.txt") ] - input[1] = FUSIONREPORT_DOWNLOAD.out.fusionreport_db - + input[1] = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref input[2] = 1 """ } @@ -91,7 +90,7 @@ nextflow_process { file("https://github.com/Clinical-Genomics/fusion-report/raw/master/tests/test_data/fusioncatcher.txt") ] - input[1] = FUSIONREPORT_DOWNLOAD.out.fusionreport_db + input[1] = FUSIONREPORT_DOWNLOAD.out.fusionreport_ref input[2] = 1 """ diff --git a/modules/local/fusionreport/detect/tests/main.nf.test.snap b/modules/local/fusionreport/detect/tests/main.nf.test.snap index fb37037f..21d16b61 100644 --- a/modules/local/fusionreport/detect/tests/main.nf.test.snap +++ b/modules/local/fusionreport/detect/tests/main.nf.test.snap @@ -68,7 +68,7 @@ "content": [ { "0": [ - "versions.yml:md5,6bd28f2526774f519a7627a30c6a7f2f" + "versions.yml:md5,8cabeb934dbeb51399427d83c57bf1b4" ], "1": [ [ @@ -173,7 +173,7 @@ ] ], "versions": [ - "versions.yml:md5,6bd28f2526774f519a7627a30c6a7f2f" + "versions.yml:md5,8cabeb934dbeb51399427d83c57bf1b4" ] } ], @@ -181,6 +181,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-06T13:12:32.981394201" + "timestamp": "2024-12-10T14:55:14.475834" } } \ No newline at end of file diff --git a/modules/local/fusionreport/download/tests/main.nf.test b/modules/local/fusionreport/download/tests/main.nf.test index dd079587..35af2a52 100644 --- a/modules/local/fusionreport/download/tests/main.nf.test +++ b/modules/local/fusionreport/download/tests/main.nf.test @@ -19,10 +19,10 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.fusionreport_db[0][1]).resolve("fusiongdb2.db"), - path(process.out.fusionreport_db[0][1]).resolve("mitelman.db"), - path(process.out.fusionreport_db[0][1]).resolve("DB-timestamp.txt").exists(), - path(process.out.fusionreport_db[0][1]).resolve("fusion_report.log").exists(), + path(process.out.fusionreport_ref[0][1]).resolve("fusiongdb2.db"), + path(process.out.fusionreport_ref[0][1]).resolve("mitelman.db"), + path(process.out.fusionreport_ref[0][1]).resolve("DB-timestamp.txt").exists(), + path(process.out.fusionreport_ref[0][1]).resolve("fusion_report.log").exists(), process.out.versions ).match() } ) diff --git a/modules/local/fusionreport/download/tests/main.nf.test.snap b/modules/local/fusionreport/download/tests/main.nf.test.snap index c328f748..79778806 100644 --- a/modules/local/fusionreport/download/tests/main.nf.test.snap +++ b/modules/local/fusionreport/download/tests/main.nf.test.snap @@ -21,7 +21,7 @@ "0": [ [ { - "id": "fusionreport_dbs" + "id": "fusion_report_db" }, [ "DB-timestamp.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -35,10 +35,10 @@ "1": [ "versions.yml:md5,fa5f13c563f431912048c1802b5a0c74" ], - "fusionreport_db": [ + "fusion_report_db": [ [ { - "id": "fusionreport_dbs" + "id": "fusion_report_db" }, [ "DB-timestamp.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -60,4 +60,4 @@ }, "timestamp": "2024-12-05T19:35:49.629287874" } -} \ No newline at end of file +} From 82c1fc01a58dec24c61b8756ad2a530a12b54ae0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 10 Dec 2024 15:12:18 +0100 Subject: [PATCH 5/6] update download snapshot --- modules/local/fusionreport/download/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/fusionreport/download/tests/main.nf.test.snap b/modules/local/fusionreport/download/tests/main.nf.test.snap index 79778806..722d8c68 100644 --- a/modules/local/fusionreport/download/tests/main.nf.test.snap +++ b/modules/local/fusionreport/download/tests/main.nf.test.snap @@ -35,7 +35,7 @@ "1": [ "versions.yml:md5,fa5f13c563f431912048c1802b5a0c74" ], - "fusion_report_db": [ + "fusionreport_ref": [ [ { "id": "fusion_report_db" @@ -58,6 +58,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T19:35:49.629287874" + "timestamp": "2024-12-10T15:05:22.781845" } -} +} \ No newline at end of file From 87f5ff80b4b69f74e9d16a08acfa62845d2856d3 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 10 Dec 2024 15:14:22 +0100 Subject: [PATCH 6/6] update detect snapshot --- modules/local/fusionreport/detect/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/fusionreport/detect/tests/main.nf.test.snap b/modules/local/fusionreport/detect/tests/main.nf.test.snap index 21d16b61..c20e3ec4 100644 --- a/modules/local/fusionreport/detect/tests/main.nf.test.snap +++ b/modules/local/fusionreport/detect/tests/main.nf.test.snap @@ -68,7 +68,7 @@ "content": [ { "0": [ - "versions.yml:md5,8cabeb934dbeb51399427d83c57bf1b4" + "versions.yml:md5,6bd28f2526774f519a7627a30c6a7f2f" ], "1": [ [ @@ -173,7 +173,7 @@ ] ], "versions": [ - "versions.yml:md5,8cabeb934dbeb51399427d83c57bf1b4" + "versions.yml:md5,6bd28f2526774f519a7627a30c6a7f2f" ] } ], @@ -181,6 +181,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-10T14:55:14.475834" + "timestamp": "2024-12-10T15:13:58.414161" } } \ No newline at end of file