From f06a085e79950ae2c9c5b4a63efcba2c38aeb7ec Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 03:52:54 +0000 Subject: [PATCH 01/15] Update multiqc config to differentate between yml patterns. --- modules/local/multiqc_mappings_config/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config/main.nf index 8efe1caa..5d809e52 100644 --- a/modules/local/multiqc_mappings_config/main.nf +++ b/modules/local/multiqc_mappings_config/main.nf @@ -10,7 +10,7 @@ process MULTIQC_MAPPINGS_CONFIG { path csv output: - path "*yml" , emit: yml + path "*config.yml" , emit: yml path "versions.yml", emit: versions script: From add5581dfa2a6a0517d5b2b9599f711bbd103977 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 03:54:24 +0000 Subject: [PATCH 02/15] Update prefetch for TES compliance. --- modules.json | 2 +- .../nf-core/sratools/prefetch/environment.yml | 2 - modules/nf-core/sratools/prefetch/main.nf | 14 ++++++- modules/nf-core/sratools/prefetch/meta.yml | 1 + .../sratools/prefetch/tests/main.nf.test | 22 ++++++++++ .../sratools/prefetch/tests/main.nf.test.snap | 41 ++++++++++++++++++- 6 files changed, 77 insertions(+), 5 deletions(-) diff --git a/modules.json b/modules.json index c6b234bb..198c9374 100644 --- a/modules.json +++ b/modules.json @@ -18,7 +18,7 @@ }, "sratools/prefetch": { "branch": "master", - "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec", + "git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "untar": { diff --git a/modules/nf-core/sratools/prefetch/environment.yml b/modules/nf-core/sratools/prefetch/environment.yml index 0abad336..6596bc7c 100644 --- a/modules/nf-core/sratools/prefetch/environment.yml +++ b/modules/nf-core/sratools/prefetch/environment.yml @@ -1,8 +1,6 @@ -name: sratools_prefetch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sra-tools=3.1.0 - conda-forge::curl=8.5.0 diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 170f1753..74838d53 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -13,7 +13,7 @@ process SRATOOLS_PREFETCH { path certificate output: - tuple val(meta), path(id), emit: sra + tuple val(meta), path(id, type: 'dir'), emit: sra path 'versions.yml' , emit: versions when: @@ -32,4 +32,16 @@ process SRATOOLS_PREFETCH { } template 'retry_with_backoff.sh' + + stub: + """ + mkdir $id + touch $id/${id}.sra + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+') + curl: \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml index ff54229f..7ed42d49 100644 --- a/modules/nf-core/sratools/prefetch/meta.yml +++ b/modules/nf-core/sratools/prefetch/meta.yml @@ -54,3 +54,4 @@ authors: - "@Midnighter" maintainers: - "@Midnighter" + - "@gallvp" diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test index f59de7cb..92034d40 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test @@ -46,4 +46,26 @@ nextflow_process { ) } } + + test("sratools/prefetch/stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ]) + input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) + input[2] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index 67795ebb..82a1969c 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -1,4 +1,43 @@ { + "sratools/prefetch/stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "DRR000774.sra:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + ], + "sra": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "DRR000774.sra:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-17T20:07:31.627115" + }, "sratools/prefetch with sralite": { "content": [ { @@ -77,4 +116,4 @@ }, "timestamp": "2024-02-28T11:48:37.428307" } -} +} \ No newline at end of file From e922b3e649f6f6b93f561a0dba591167a6bd77d0 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 04:00:54 +0000 Subject: [PATCH 03/15] Update changelog. --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index dbfb81be..6abb8554 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check +- [PR #320](https://github.com/nf-core/fetchngs/pull/20) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance ### Software dependencies @@ -40,6 +41,7 @@ Special thanks to the following for their contributions to the release: - [Maxime Garcia](https://github.com/maxulysse) - [Sateesh Peri](https://github.com/sateeshperi) - [Sebastian Uhrig](https://github.com/suhrig) +- [Venkat Malladi](https://github.com/vsmalladi) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. From 89935ad1fcbe8a4c501fcb1ea966638ee74ab4bc Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 04:08:07 +0000 Subject: [PATCH 04/15] Fix linting issues. --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/linting.yml | 19 +++++++++---------- .github/workflows/linting_comment.yml | 2 +- 3 files changed, 11 insertions(+), 12 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 4dde8d56..72c2b4ae 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/fetc - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/fetchngs/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/fetchngs _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 073e1876..1fcafe88 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,13 +14,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 - cache: "pip" + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit @@ -32,14 +31,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - name: Install dependencies @@ -60,7 +59,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index b706875f..40acc23f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 + uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 with: workflow: linting.yml workflow_conclusion: completed From e4b2c5cffb36ad52cb7e965208d8c9c21620417f Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 04:35:11 +0000 Subject: [PATCH 05/15] Update snapshot for multiqc_mappings_config. --- .../tests/main.nf.test.snap | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) 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 43e46f61..fcd07b02 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -3,29 +3,23 @@ "content": [ { "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a" ], "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + "versions.yml:md5,c75e3e07b124e83f49a44d9bc31bd8e8" ], "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + "versions.yml:md5,c75e3e07b124e83f49a44d9bc31bd8e8" ], "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:52:12.65888" + "timestamp": "2024-09-16T04:34:17.43270068" } } \ No newline at end of file From 81f1f4a137613b81f7cd9af4573cde92fcc4be0b Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 06:22:11 +0000 Subject: [PATCH 06/15] Update snapshots. --- .../local/aspera_cli/tests/main.nf.test.snap | 60 +++-------------- .../sra_fastq_ftp/tests/main.nf.test.snap | 10 +-- .../tests/main.nf.test.snap | 8 +-- .../tests/main.nf.test.snap | 8 +-- .../tests/main.nf.test.snap | 6 +- .../fasterqdump/tests/main.nf.test.snap | 54 ++++------------ .../sratools/prefetch/tests/main.nf.test.snap | 64 +++++-------------- 7 files changed, 52 insertions(+), 158 deletions(-) diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap index 0ba6a643..462585e3 100644 --- a/modules/local/aspera_cli/tests/main.nf.test.snap +++ b/modules/local/aspera_cli/tests/main.nf.test.snap @@ -3,73 +3,29 @@ "content": [ { "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", - "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" - ] - ] + ], "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] + ], "2": [ - "versions.yml:md5,a51a1dfc6308d71058ddc12c46101dd3" + ], "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", - "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" - ] - ] + ], "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] + ], "versions": [ - "versions.yml:md5,a51a1dfc6308d71058ddc12c46101dd3" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:52:00.601018" + "timestamp": "2024-09-16T04:48:03.248398219" } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap index 229ad4fe..681a20c8 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -31,7 +31,7 @@ ] ], "2": [ - "versions.yml:md5,7bfc86ca1f3e3236dbb91eb85c1d7af0" + "versions.yml:md5,0642085ed317ac363ce5f3a3605d22df" ], "fastq": [ [ @@ -62,14 +62,14 @@ ] ], "versions": [ - "versions.yml:md5,7bfc86ca1f3e3236dbb91eb85c1d7af0" + "versions.yml:md5,0642085ed317ac363ce5f3a3605d22df" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:51:51.301654" + "timestamp": "2024-09-16T04:48:13.37244363" } -} +} \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap index f7b6cee5..939f1548 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -6,20 +6,20 @@ "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" ], "1": [ - "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" + "versions.yml:md5,452af3b6d74d1de88f851d78473df8d4" ], "tsv": [ "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" ], "versions": [ - "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" + "versions.yml:md5,452af3b6d74d1de88f851d78473df8d4" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:52:05.345153" + "timestamp": "2024-09-16T04:47:54.693964769" } } \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap index be190f5a..82f63709 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -6,20 +6,20 @@ "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" ], "1": [ - "versions.yml:md5,e95f8185f665127a73622a19d321bcca" + "versions.yml:md5,87be2d8760490c5b0329a8710644b4e3" ], "tsv": [ "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" ], "versions": [ - "versions.yml:md5,e95f8185f665127a73622a19d321bcca" + "versions.yml:md5,87be2d8760490c5b0329a8710644b4e3" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:51:45.748227" + "timestamp": "2024-09-16T04:48:35.453829086" } } \ No newline at end of file diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap index 5e314f0b..396c39c8 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap @@ -2,13 +2,13 @@ "Should run without failures": { "content": [ [ - "versions.yml:md5,3d6ee88cce1ee517e198633f062589a8" + "versions.yml:md5,7c79d8a8b8e752bb3fc96b5ff08ae45e" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:47:15.824443" + "timestamp": "2024-09-16T05:22:47.930655145" } } \ No newline at end of file diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap index ce0f9800..de7d0a5f 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap @@ -3,76 +3,46 @@ "content": [ { "0": [ - [ - { - "id": "test_single_end", - "single_end": true - }, - "test_single_end.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887" - ] + ], "1": [ - "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" + ], "reads": [ - [ - { - "id": "test_single_end", - "single_end": true - }, - "test_single_end.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887" - ] + ], "versions": [ - "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T15:25:52.837288" + "timestamp": "2024-09-16T04:50:04.981225374" }, "Paired-end": { "content": [ { "0": [ - [ - { - "id": "test_paired_end", - "single_end": false - }, - [ - "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c", - "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311" - ] - ] + ], "1": [ - "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" + ], "reads": [ - [ - { - "id": "test_paired_end", - "single_end": false - }, - [ - "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c", - "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311" - ] - ] + ], "versions": [ - "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T15:26:42.466223" + "timestamp": "2024-09-16T04:50:20.779727834" } } \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index 82a1969c..22641820 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ] ], "1": [ - "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + "versions.yml:md5,afc103d69e2f31782637d7d91eba69b0" ], "sra": [ [ @@ -28,92 +28,60 @@ ] ], "versions": [ - "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + "versions.yml:md5,afc103d69e2f31782637d7d91eba69b0" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T20:07:31.627115" + "timestamp": "2024-09-16T05:23:51.982828628" }, "sratools/prefetch with sralite": { "content": [ { "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" - ] - ] + ], "1": [ - "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + ], "sra": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" - ] - ] + ], "versions": [ - "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:49:02.309737" + "timestamp": "2024-09-16T04:49:40.146972356" }, "sratools/prefetch": { "content": [ { "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" - ] - ] + ], "1": [ - "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + ], "sra": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" - ] - ] + ], "versions": [ - "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T11:48:37.428307" + "timestamp": "2024-09-16T04:49:13.529179115" } } \ No newline at end of file From 20f2fb028b30b8e8a38028ea56dc163bdd2d7363 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 17:52:24 +0000 Subject: [PATCH 07/15] Update Snapshots. --- .../custom/sratoolsncbisettings/tests/main.nf.test.snap | 4 ++-- modules/nf-core/sratools/prefetch/tests/main.nf.test.snap | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap index 396c39c8..4b3309d4 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap @@ -2,13 +2,13 @@ "Should run without failures": { "content": [ [ - "versions.yml:md5,7c79d8a8b8e752bb3fc96b5ff08ae45e" + "versions.yml:md5,bc8238c8fcfbd7d5d4d32614fcf0027a" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T05:22:47.930655145" + "timestamp": "2024-09-16T16:47:47.694358192" } } \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index 22641820..abd8a2c6 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ] ], "1": [ - "versions.yml:md5,afc103d69e2f31782637d7d91eba69b0" + "versions.yml:md5,c4e05d768270116a7245de847f18ad5a" ], "sra": [ [ @@ -28,7 +28,7 @@ ] ], "versions": [ - "versions.yml:md5,afc103d69e2f31782637d7d91eba69b0" + "versions.yml:md5,c4e05d768270116a7245de847f18ad5a" ] } ], @@ -36,7 +36,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T05:23:51.982828628" + "timestamp": "2024-09-16T16:48:51.621717763" }, "sratools/prefetch with sralite": { "content": [ From ab0300abcfa33ebde0f3a0ca67e0437e709d4f4c Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 16 Sep 2024 18:54:46 +0000 Subject: [PATCH 08/15] Update snap. --- modules/nf-core/sratools/prefetch/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index abd8a2c6..bb220f43 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ] ], "1": [ - "versions.yml:md5,c4e05d768270116a7245de847f18ad5a" + "versions.yml:md5,a0ee57d5fe8e91604aa93b136db0d7b3" ], "sra": [ [ @@ -28,7 +28,7 @@ ] ], "versions": [ - "versions.yml:md5,c4e05d768270116a7245de847f18ad5a" + "versions.yml:md5,a0ee57d5fe8e91604aa93b136db0d7b3" ] } ], @@ -36,7 +36,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T16:48:51.621717763" + "timestamp": "2024-09-16T18:42:07.112577866" }, "sratools/prefetch with sralite": { "content": [ From d4355dd52ab0c038bc7e1491516482e0b6aac340 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 17 Sep 2024 10:40:05 -0500 Subject: [PATCH 09/15] Fix snapshots. --- .../local/aspera_cli/tests/main.nf.test.snap | 60 ++++++++++++++--- .../tests/main.nf.test.snap | 8 +-- .../sra_fastq_ftp/tests/main.nf.test.snap | 8 +-- .../tests/main.nf.test.snap | 8 +-- .../tests/main.nf.test.snap | 8 +-- .../tests/main.nf.test.snap | 6 +- .../fasterqdump/tests/main.nf.test.snap | 54 ++++++++++++---- .../sratools/prefetch/tests/main.nf.test.snap | 64 ++++++++++++++----- 8 files changed, 161 insertions(+), 55 deletions(-) diff --git a/modules/local/aspera_cli/tests/main.nf.test.snap b/modules/local/aspera_cli/tests/main.nf.test.snap index 462585e3..ff8acd4c 100644 --- a/modules/local/aspera_cli/tests/main.nf.test.snap +++ b/modules/local/aspera_cli/tests/main.nf.test.snap @@ -3,29 +3,73 @@ "content": [ { "0": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", + "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" + ] + ] ], "1": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] ], "2": [ - + "versions.yml:md5,a51a1dfc6308d71058ddc12c46101dd3" ], "fastq": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848", + "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32" + ] + ] ], "md5": [ - + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] ], "versions": [ - + "versions.yml:md5,a51a1dfc6308d71058ddc12c46101dd3" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:48:03.248398219" + "timestamp": "2024-09-17T09:16:31.501413" } } \ No newline at end of file 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 fcd07b02..9862693f 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -6,10 +6,10 @@ "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a" ], "1": [ - "versions.yml:md5,c75e3e07b124e83f49a44d9bc31bd8e8" + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" ], "versions": [ - "versions.yml:md5,c75e3e07b124e83f49a44d9bc31bd8e8" + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" ], "yml": [ "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a" @@ -17,9 +17,9 @@ } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:34:17.43270068" + "timestamp": "2024-09-17T09:16:46.557614" } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap index 681a20c8..0449978f 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -31,7 +31,7 @@ ] ], "2": [ - "versions.yml:md5,0642085ed317ac363ce5f3a3605d22df" + "versions.yml:md5,7bfc86ca1f3e3236dbb91eb85c1d7af0" ], "fastq": [ [ @@ -62,14 +62,14 @@ ] ], "versions": [ - "versions.yml:md5,0642085ed317ac363ce5f3a3605d22df" + "versions.yml:md5,7bfc86ca1f3e3236dbb91eb85c1d7af0" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:48:13.37244363" + "timestamp": "2024-09-17T09:16:57.715689" } } \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap index 939f1548..413f42a8 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -6,20 +6,20 @@ "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" ], "1": [ - "versions.yml:md5,452af3b6d74d1de88f851d78473df8d4" + "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" ], "tsv": [ "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" ], "versions": [ - "versions.yml:md5,452af3b6d74d1de88f851d78473df8d4" + "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:47:54.693964769" + "timestamp": "2024-09-17T09:17:11.040523" } } \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap index 82f63709..a4090ef3 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -6,20 +6,20 @@ "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" ], "1": [ - "versions.yml:md5,87be2d8760490c5b0329a8710644b4e3" + "versions.yml:md5,e95f8185f665127a73622a19d321bcca" ], "tsv": [ "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" ], "versions": [ - "versions.yml:md5,87be2d8760490c5b0329a8710644b4e3" + "versions.yml:md5,e95f8185f665127a73622a19d321bcca" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:48:35.453829086" + "timestamp": "2024-09-17T09:17:23.371547" } } \ No newline at end of file diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap index 4b3309d4..158ac449 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap +++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap @@ -2,13 +2,13 @@ "Should run without failures": { "content": [ [ - "versions.yml:md5,bc8238c8fcfbd7d5d4d32614fcf0027a" + "versions.yml:md5,3d6ee88cce1ee517e198633f062589a8" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T16:47:47.694358192" + "timestamp": "2024-09-17T09:17:35.745689" } } \ No newline at end of file diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap index de7d0a5f..927eef7f 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap @@ -3,46 +3,76 @@ "content": [ { "0": [ - + [ + { + "id": "test_single_end", + "single_end": true + }, + "test_single_end.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887" + ] ], "1": [ - + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ], "reads": [ - + [ + { + "id": "test_single_end", + "single_end": true + }, + "test_single_end.fastq.gz:md5,674d78c1cc3c1308d6d39d6369a42887" + ] ], "versions": [ - + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:50:04.981225374" + "timestamp": "2024-09-17T09:18:32.518988" }, "Paired-end": { "content": [ { "0": [ - + [ + { + "id": "test_paired_end", + "single_end": false + }, + [ + "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c", + "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311" + ] + ] ], "1": [ - + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ], "reads": [ - + [ + { + "id": "test_paired_end", + "single_end": false + }, + [ + "test_paired_end_1.fastq.gz:md5,8573015c91d099b6e30789f8bab2f43c", + "test_paired_end_2.fastq.gz:md5,37e6f719a022dc3c9994c80fbc20c311" + ] + ] ], "versions": [ - + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:50:20.779727834" + "timestamp": "2024-09-17T09:21:08.795572" } } \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap index bb220f43..fd12e79e 100644 --- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ] ], "1": [ - "versions.yml:md5,a0ee57d5fe8e91604aa93b136db0d7b3" + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" ], "sra": [ [ @@ -28,60 +28,92 @@ ] ], "versions": [ - "versions.yml:md5,a0ee57d5fe8e91604aa93b136db0d7b3" + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T18:42:07.112577866" + "timestamp": "2024-09-17T09:24:17.373992" }, "sratools/prefetch with sralite": { "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": false + }, + [ + "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" + ] + ] ], "1": [ - + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" ], "sra": [ - + [ + { + "id": "test", + "single_end": false + }, + [ + "SRR1170046.sralite:md5,7acfce556ca0951aff49d780899c105b" + ] + ] ], "versions": [ - + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:49:40.146972356" + "timestamp": "2024-09-17T09:24:02.118978" }, "sratools/prefetch": { "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": false + }, + [ + "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" + ] + ] ], "1": [ - + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" ], "sra": [ - + [ + { + "id": "test", + "single_end": false + }, + [ + "DRR000774.sra:md5,7647dba20c89c0e3d7ad13842f060eb0" + ] + ] ], "versions": [ - + "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T04:49:13.529179115" + "timestamp": "2024-09-17T09:21:54.739086" } } \ No newline at end of file From 63003d941f3885664a51f080708ac12caff8f64f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 09:32:10 +0200 Subject: [PATCH 10/15] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f2c089d..01377bbb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check - [PR #316](https://github.com/nf-core/fetchngs/pull/316) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD -- [PR #320](https://github.com/nf-core/fetchngs/pull/20) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance +- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance ### Software dependencies From 0987c8ccacbc094e8fb91f3cb78d2637b0541398 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 13:07:07 +0200 Subject: [PATCH 11/15] Fix manifest --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 13145549..b69fc9b5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -248,7 +248,7 @@ validation { \033[0;35m ${manifest.name} ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x From 473d1a2c2e0ffa040ad649cf2c7cf53412e535e3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 15 Oct 2024 13:07:27 +0200 Subject: [PATCH 12/15] attempt to fix tests: 1 --- workflows/sra/tests/main.nf.test | 27 +- workflows/sra/tests/main.nf.test.snap | 281 ++++++++++++++++++ .../sra_custom_ena_metadata_fields.nf.test | 35 +-- ...ra_custom_ena_metadata_fields.nf.test.snap | 125 ++++++++ .../tests/sra_download_method_aspera.nf.test | 31 +- .../sra_download_method_aspera.nf.test.snap | 281 ++++++++++++++++++ .../sra_download_method_sratools.nf.test | 31 +- .../sra_download_method_sratools.nf.test.snap | 281 ++++++++++++++++++ .../sra_nf_core_pipeline_atacseq.nf.test | 31 +- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 281 ++++++++++++++++++ .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 31 +- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 281 ++++++++++++++++++ .../sra_nf_core_pipeline_taxprofiler.nf.test | 31 +- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 281 ++++++++++++++++++ .../sra_nf_core_pipeline_viralrecon.nf.test | 31 +- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 281 ++++++++++++++++++ .../sra/tests/sra_skip_fastq_download.nf.test | 31 +- .../sra_skip_fastq_download.nf.test.snap | 279 +++++++++++++++++ 18 files changed, 2426 insertions(+), 224 deletions(-) create mode 100644 workflows/sra/tests/main.nf.test.snap create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap create mode 100644 workflows/sra/tests/sra_download_method_aspera.nf.test.snap create mode 100644 workflows/sra/tests/sra_download_method_sratools.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 1e2856c1..6704652c 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -15,6 +15,9 @@ nextflow_workflow { test("Parameters: default") { when { + params { + outdir = "$outputDir" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") @@ -23,29 +26,9 @@ nextflow_workflow { } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap new file mode 100644 index 00000000..17beee5d --- /dev/null +++ b/workflows/sra/tests/main.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: default": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T12:58:48.512328" + } +} \ 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 c8d17876..1aa68be2 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -15,42 +15,23 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { when { + params { + outdir = "$outputDir" + ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" + nf_core_pipeline = "rnaseq" + sample_mapping_fields = "run_accession,library_layout" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "rnaseq" - ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" - sample_mapping_fields = "run_accession,library_layout" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('SINGLE') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('SINGLE') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "3b70bc9658eab4ba2f4ec98cb749ac9d" - } - } + { assert workflow.success}, + { assert snapshot(workflow.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 new file mode 100644 index 00000000..b85b2dd4 --- /dev/null +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -0,0 +1,125 @@ +{ + "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139" + ], + "1": [ + "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac" + ], + "2": [ + "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d" + ], + "3": [ + { + "experiment_accession": "DRX026011", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "library_layout": "PAIRED", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "run_accession": "DRR028935", + "single_end": false + }, + { + "experiment_accession": "ERX1234253", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "library_layout": "SINGLE", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "run_accession": "ERR1160846", + "single_end": true + }, + { + "experiment_accession": "SRX6725035", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "library_layout": "SINGLE", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "run_accession": "SRR9984183", + "single_end": true + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d" + ], + "samplesheet": [ + "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139" + ], + "sra_metadata": [ + { + "experiment_accession": "DRX026011", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "library_layout": "PAIRED", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "run_accession": "DRR028935", + "single_end": false + }, + { + "experiment_accession": "ERX1234253", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "library_layout": "SINGLE", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "run_accession": "ERR1160846", + "single_end": true + }, + { + "experiment_accession": "SRX6725035", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "library_layout": "SINGLE", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "run_accession": "SRR9984183", + "single_end": true + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:03:36.272997" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test index d431a571..b6bc42af 100644 --- a/workflows/sra/tests/sra_download_method_aspera.nf.test +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --download_method aspera") { when { + params { + outdir = "$outputDir" + download_method = 'aspera' + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - download_method = 'aspera' - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test.snap b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap new file mode 100644 index 00000000..04a630a8 --- /dev/null +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --download_method aspera": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,d0f905867fa38eb136c88285669900c5" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": 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b/workflows/sra/tests/sra_download_method_sratools.nf.test index e4f8c2d2..33e048a5 100644 --- a/workflows/sra/tests/sra_download_method_sratools.nf.test +++ b/workflows/sra/tests/sra_download_method_sratools.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --download_method sratools") { when { + params { + outdir = "$outputDir" + download_method = 'sratools' + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - download_method = 'sratools' - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test.snap b/workflows/sra/tests/sra_download_method_sratools.nf.test.snap new file mode 100644 index 00000000..2203c2e0 --- /dev/null +++ b/workflows/sra/tests/sra_download_method_sratools.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --download_method sratools": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,1dc8ec98b2cc2d9f07ebd0f033c5e4eb" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,1c3a691ea99767f25de2492440a02cb7", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,6fa02d3e52613cfe3464cc7a29f227d4", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + 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a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 72f8d595..886aef19 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline atacseq") { when { + params { + outdir = "$outputDir" + nf_core_pipeline = "atacseq" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "atacseq" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"replicate"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert 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path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"strandedness"' , '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.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 new file mode 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"fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:05:35.712529" + } +} \ 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 50650b79..257afef5 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline taxprofiler") { when { + params { + outdir = "$outputDir" + nf_core_pipeline = "taxprofiler" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "taxprofiler" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(5) == ['"sample"', '"fastq_1"', '"fastq_2"', '"fasta"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.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 new file mode 100644 index 00000000..d4d7047e --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --nf_core_pipeline taxprofiler": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,790f0cad9d01e35e0d1e03f199851770" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,790f0cad9d01e35e0d1e03f199851770" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:05:55.50559" + } +} \ 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 1fe9cc41..77ab9e2a 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -15,40 +15,21 @@ nextflow_workflow { test("Parameters: --nf_core_pipeline viralrecon") { when { + params { + outdir = "$outputDir" + nf_core_pipeline = "viralrecon" + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - nf_core_pipeline = "viralrecon" - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.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 new file mode 100644 index 00000000..a9b14b4d --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -0,0 +1,281 @@ +{ + "Parameters: --nf_core_pipeline viralrecon": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,d81fe6175afaa01183475a6e28c7caa9" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "4": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ], + "mappings": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "sample_mappings": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "samplesheet": [ + "samplesheet.csv:md5,d81fe6175afaa01183475a6e28c7caa9" + ], + "sra_metadata": [ + { + "base_count": "194930", + "experiment_accession": "DRX026011", + "experiment_alias": "DRX026011", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing: Illumina HiSeq 2500 paired end sequencing of SAMD00024405", + "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", + "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_bytes": "60275;61610", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz", + "fastq_md5": "cc01df82a9354bb6b3be93483b20c35a;941c9998d746416dad53c94c480ddf30", + "id": "DRX026011_DRR028935", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "PAIRED", + "library_name": "day0_BbSQE-I", + "library_selection": "cDNA", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "RNA-Seq", + "md5_1": "cc01df82a9354bb6b3be93483b20c35a", + "md5_2": "941c9998d746416dad53c94c480ddf30", + "read_count": "965", + "run_accession": "DRR028935", + "run_alias": "DRR028935", + "sample_accession": "SAMD00024405", + "sample_alias": "SAMD00024405", + "sample_description": "Liquid culture", + "sample_title": "Botryococcus braunii Showa at day 0 after inoculation into fresh culture medium", + "scientific_name": "Botryococcus braunii Showa", + "secondary_sample_accession": "DRS019431", + "secondary_study_accession": "DRP002616", + "single_end": false, + "study_accession": "PRJDB3420", + "study_alias": "DRP002616", + "study_title": "Liquid culture of Botryococcus braunii, race B, Showa", + "submission_accession": "DRA002949", + "tax_id": "1202541" + }, + { + "base_count": "1996273", + "experiment_accession": "SRX6725035", + "experiment_alias": "Emb289P1_bin131", + "experiment_title": "Illumina HiSeq 2500 sequencing: Binning of metagenomic reads from the P1 gut compartment of Embiratermes neotenicus", + "fastq_1": "SRX6725035_SRR9984183.fastq.gz:md5,c9b4c2c4abf19da7082caf442fdefea7", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_bytes": "605358", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR998/003/SRR9984183/SRR9984183.fastq.gz", + "fastq_md5": "0b512d2dc31685983456bd56fd836544", + "id": "SRX6725035_SRR9984183", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "Emb289P1_bin131", + "library_selection": "RANDOM", + "library_source": "METAGENOMIC", + "library_strategy": "WGS", + "md5_1": "0b512d2dc31685983456bd56fd836544", + "md5_2": "", + "read_count": "58", + "run_accession": "SRR9984183", + "run_alias": "Emb289P1_bin131.fastq", + "sample_accession": "SAMN12581720", + "sample_alias": "Emb289P1_bin131", + "sample_description": "Keywords: GSC:MIxS MIMAG:5.0", + "sample_title": "MIMAG Metagenome-assembled Genome sample from Defluviitaleaceae bacterium", + "scientific_name": "Defluviitaleaceae bacterium", + "secondary_sample_accession": "SRS5277011", + "secondary_study_accession": "SRP218535", + "single_end": true, + "study_accession": "PRJNA560329", + "study_alias": "PRJNA560329", + "study_title": "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites", + "submission_accession": "SRA942061", + "tax_id": "2660712" + }, + { + "base_count": "35658", + "experiment_accession": "ERX1234253", + "experiment_alias": "qiita_ptid_1263:10317.BLANK.93.3E.r22", + "experiment_title": "Illumina HiSeq 2500 sequencing: qiita_ptid_1263:10317.BLANK.93.3E.r22", + "fastq_1": "ERX1234253_ERR1160846.fastq.gz:md5,b1de59f829fbd2d60a1ed4bc3da55709", + "fastq_2": "", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_bytes": "18077", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/006/ERR1160846/ERR1160846.fastq.gz", + "fastq_md5": "5924f20ef547ebdfed7cad795bbab6e6", + "id": "ERX1234253_ERR1160846", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "library_layout": "SINGLE", + "library_name": "10317.BLANK.93.3E.r22", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "md5_1": "5924f20ef547ebdfed7cad795bbab6e6", + "md5_2": "", + "read_count": "283", + "run_accession": "ERR1160846", + "run_alias": "qiita_ppdid_706:10317.BLANK.93.3E.r22", + "sample_accession": "SAMEA3687214", + "sample_alias": "qiita_sid_10317:10317.BLANK.93.3E.r22", + "sample_description": "American Gut control", + "sample_title": "10317.BLANK.93.3E.r22", + "scientific_name": "metagenome", + "secondary_sample_accession": "ERS994363", + "secondary_study_accession": "ERP012803", + "single_end": true, + "study_accession": "PRJEB11419", + "study_alias": "qiita_sid_10317", + "study_title": "American Gut Project", + "submission_accession": "ERA541392", + "tax_id": "256318" + } + ], + "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.2" + }, + "timestamp": "2024-10-15T13:06:17.713513" + } +} \ 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 8663cf3f..4b7080d9 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -14,40 +14,21 @@ nextflow_workflow { test("Parameters: --skip_fastq_download") { when { + params { + outdir = "$outputDir" + skip_fastq_download = true + } workflow { """ input[0] = Channel.from("DRX026011", "ERX1234253", "SRX6725035") """ } - params { - skip_fastq_download = true - } } then { - assert workflow.success - assertAll( - { - with(workflow.out.samplesheet) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',')[0].take(4) == ['"sample"', '"fastq_1"', '"fastq_2"', '"run_accession"'] - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.mappings) { - assert path(get(0)).readLines().size() == 4 - assert path(get(0)).readLines()*.split(',').collect { it[0] } == ['"sample"', '"DRX026011"', '"ERX1234253"', '"SRX6725035"'] - assert path(get(0)).text.contains('Illumina HiSeq 2500') - } - }, - { - with(workflow.out.sample_mappings) { - assert path(get(0)[0]).md5 == "1ac06bb95b503703430e74660bbdd768" - } - } + { assert workflow.success}, + { assert snapshot(workflow.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 new file mode 100644 index 00000000..34ee72c1 --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -0,0 +1,279 @@ +{ + "Parameters: --skip_fastq_download": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,0788cf0fed166518e5d1399532f8068f" + ], + "1": [ + "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" + ], + "2": [ + "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" + ], + "3": [ + { + "base_count": "194930", + "experiment_accession": 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--- workflows/sra/tests/main.nf.test | 8 +- workflows/sra/tests/main.nf.test.snap | 404 ++++++------------ .../sra_custom_ena_metadata_fields.nf.test | 8 +- ...ra_custom_ena_metadata_fields.nf.test.snap | 170 +++----- .../tests/sra_download_method_aspera.nf.test | 8 +- .../sra_download_method_aspera.nf.test.snap | 404 ++++++------------ .../sra_download_method_sratools.nf.test | 8 +- .../sra_download_method_sratools.nf.test.snap | 404 ++++++------------ .../sra_nf_core_pipeline_atacseq.nf.test | 8 +- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 404 ++++++------------ .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 8 +- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 404 ++++++------------ .../sra_nf_core_pipeline_taxprofiler.nf.test | 8 +- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 404 ++++++------------ .../sra_nf_core_pipeline_viralrecon.nf.test | 8 +- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 404 ++++++------------ .../sra/tests/sra_skip_fastq_download.nf.test | 8 +- .../sra_skip_fastq_download.nf.test.snap | 401 ++++++----------- 18 files changed, 1181 insertions(+), 2290 deletions(-) diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test index 6704652c..b0c19a25 100644 --- a/workflows/sra/tests/main.nf.test +++ b/workflows/sra/tests/main.nf.test @@ -28,7 +28,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).match() } ) } } diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap index 17beee5d..aca9cfd8 100644 --- a/workflows/sra/tests/main.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -1,281 +1,143 @@ { "Parameters: default": { "content": [ - { - "0": [ - "samplesheet.csv:md5,636ddfb5fcd882e17303628f80df98d8" - ], - "1": [ - 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"versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T12:58:48.512328" + "timestamp": "2024-10-15T13:35:40.78967" } } \ 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 1aa68be2..a4879a19 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -31,7 +31,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).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 b85b2dd4..7055b4c4 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 @@ -1,125 +1,65 @@ { "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": { "content": [ - { - "0": [ - "samplesheet.csv:md5,5f79ecf678ce5af375cf8749b56da139" - ], - "1": [ - "id_mappings.csv:md5,7345715e7db0a160efb8dd3be9ce58ac" - ], - "2": [ - "multiqc_config.yml:md5,3b70bc9658eab4ba2f4ec98cb749ac9d" - ], - "3": [ - { - "experiment_accession": "DRX026011", - "fastq_1": "DRX026011_DRR028935_1.fastq.gz:md5,f9b4a5d25aa7d6ab4050dbe0764eb04d", - "fastq_2": "DRX026011_DRR028935_2.fastq.gz:md5,dc0d2e1fc46f4d4581a477f87ec3ff15", - "fastq_ftp": 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a/workflows/sra/tests/sra_download_method_aspera.nf.test b/workflows/sra/tests/sra_download_method_aspera.nf.test index b6bc42af..62a423e0 100644 --- a/workflows/sra/tests/sra_download_method_aspera.nf.test +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test @@ -29,7 +29,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).match() } ) } } diff --git a/workflows/sra/tests/sra_download_method_aspera.nf.test.snap b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap index 04a630a8..62b8319c 100644 --- a/workflows/sra/tests/sra_download_method_aspera.nf.test.snap +++ b/workflows/sra/tests/sra_download_method_aspera.nf.test.snap @@ -1,281 +1,143 @@ { "Parameters: --download_method aspera": { "content": [ - { - "0": [ - 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"versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:04:11.866017" + "timestamp": "2024-10-15T13:36:29.262179" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_download_method_sratools.nf.test b/workflows/sra/tests/sra_download_method_sratools.nf.test index 33e048a5..74de5060 100644 --- a/workflows/sra/tests/sra_download_method_sratools.nf.test +++ b/workflows/sra/tests/sra_download_method_sratools.nf.test @@ -29,7 +29,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).match() } ) } } diff --git 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b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -29,7 +29,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).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 12c26342..f1a21171 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 @@ -1,281 +1,143 @@ { "Parameters: --nf_core_pipeline atacseq": { "content": [ - { - "0": [ - "samplesheet.csv:md5,ec54a949c41851e8c5c20dc595992d25" - ], - "1": [ - "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" - ], - "2": [ - "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" - ], - "3": [ - { 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a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 7f67aefb..f82b1755 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -29,7 +29,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).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 61f6cd12..397c85c3 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 @@ -1,281 +1,143 @@ { "Parameters: --nf_core_pipeline rnaseq": { "content": [ - { - "0": [ - 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"versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,c19fc0f920e57875881761cc944a46d7" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:05:35.712529" + "timestamp": "2024-10-15T13:37:33.713018" } } \ 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 257afef5..da15ed22 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -29,7 +29,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).match() } ) } } diff --git 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b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -29,7 +29,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).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 a9b14b4d..715cf6b8 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 @@ -1,281 +1,143 @@ { "Parameters: --nf_core_pipeline viralrecon": { "content": [ - { - "0": [ - "samplesheet.csv:md5,d81fe6175afaa01183475a6e28c7caa9" - ], - "1": [ - "id_mappings.csv:md5,3e41ce6ab19feb76f2b20fa77a910ad3" - ], - "2": [ - "multiqc_config.yml:md5,1ac06bb95b503703430e74660bbdd768" 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a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 4b7080d9..a467f59b 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -28,7 +28,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match() } + { assert snapshot( + file(workflow.out.samplesheet[0]).name, + workflow.out.mappings, + workflow.out.sample_mappings, + workflow.out.sra_metadata, + workflow.out.versions + ).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 34ee72c1..436769c1 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -1,279 +1,142 @@ { "Parameters: --skip_fastq_download": { "content": [ - { - "0": [ - 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"nextflow": "24.09.2" }, - "timestamp": "2024-10-15T13:06:36.956527" + "timestamp": "2024-10-15T13:38:24.154005" } } \ No newline at end of file From f240a7a5917e774929ec11af4dbf90a2b1b78b0a Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 13:53:13 +0200 Subject: [PATCH 14/15] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ff54ed7..8283f2ed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check - [PR #316](https://github.com/nf-core/fetchngs/pull/316) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD - [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance +- [PR #320](https://github.com/nf-core/fetchngs/pull/320) - Refactor workflow tests - [PR #323](https://github.com/nf-core/fetchngs/pull/323) - Template update for nf-core/tools v3.0.2 ### Software dependencies From d0e3777df1503646430875e7a2b3db7762c7b116 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 17:08:43 +0200 Subject: [PATCH 15/15] Update modules/local/multiqc_mappings_config/main.nf Co-authored-by: Jose Espinosa-Carrasco --- modules/local/multiqc_mappings_config/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config/main.nf index 5d809e52..ac379065 100644 --- a/modules/local/multiqc_mappings_config/main.nf +++ b/modules/local/multiqc_mappings_config/main.nf @@ -10,7 +10,7 @@ process MULTIQC_MAPPINGS_CONFIG { path csv output: - path "*config.yml" , emit: yml + path "*config.yml" , emit: yml path "versions.yml", emit: versions script: