From b7979a30b1d50ad9ffa888258a0433134a0b2c01 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 30 Jan 2024 17:36:02 +0000 Subject: [PATCH 1/3] Revert sratools fasterqdump version to fix #221 --- modules.json | 3 +- .../sratools/fasterqdump/environment.yml | 2 +- modules/nf-core/sratools/fasterqdump/main.nf | 4 +- .../fasterqdump/sratools-fasterqdump.diff | 63 +++++++++++++++++++ 4 files changed, 68 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff diff --git a/modules.json b/modules.json index 1ddaa1fb..9190e3f5 100644 --- a/modules.json +++ b/modules.json @@ -13,7 +13,8 @@ "sratools/fasterqdump": { "branch": "master", "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"], + "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff" }, "sratools/prefetch": { "branch": "master", diff --git a/modules/nf-core/sratools/fasterqdump/environment.yml b/modules/nf-core/sratools/fasterqdump/environment.yml index 4011b691..dd0faa56 100644 --- a/modules/nf-core/sratools/fasterqdump/environment.yml +++ b/modules/nf-core/sratools/fasterqdump/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::sra-tools=3.0.8 + - bioconda::sra-tools=2.11.0 - conda-forge::pigz=2.6 diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf index d4ddf268..e7cf157a 100644 --- a/modules/nf-core/sratools/fasterqdump/main.nf +++ b/modules/nf-core/sratools/fasterqdump/main.nf @@ -4,8 +4,8 @@ process SRATOOLS_FASTERQDUMP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' : - 'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : + 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }" input: tuple val(meta), path(sra) diff --git a/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff new file mode 100644 index 00000000..1fb8cbf4 --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff @@ -0,0 +1,63 @@ +Changes in module 'nf-core/sratools/fasterqdump' +--- modules/nf-core/sratools/fasterqdump/main.nf ++++ modules/nf-core/sratools/fasterqdump/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' : +- 'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }" ++ 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' : ++ 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }" + + input: + tuple val(meta), path(sra) + +--- /dev/null ++++ modules/nf-core/sratools/fasterqdump/nextflow.config +@@ -0,0 +1,10 @@ ++process { ++ withName: SRATOOLS_FASTERQDUMP { ++ ext.args = '--split-files --include-technical' ++ publishDir = [ ++ path: { "${params.outdir}/fastq" }, ++ mode: params.publish_dir_mode, ++ pattern: "*.fastq.gz" ++ ] ++ } ++} +--- modules/nf-core/sratools/fasterqdump/environment.yml ++++ modules/nf-core/sratools/fasterqdump/environment.yml +@@ -4,5 +4,5 @@ + - bioconda + - defaults + dependencies: +- - bioconda::sra-tools=3.0.8 ++ - bioconda::sra-tools=2.11.0 + - conda-forge::pigz=2.6 + +--- modules/nf-core/sratools/fasterqdump/tests/main.nf.test ++++ modules/nf-core/sratools/fasterqdump/tests/main.nf.test +@@ -3,11 +3,9 @@ + script "../main.nf" + config "./nextflow.config" + process "SRATOOLS_FASTERQDUMP" +- tag "modules" +- tag "modules_nfcore" +- tag "untar" +- tag "sratools" +- tag "sratools/fasterqdump" ++ tag "SRATOOLS_FASTERQDUMP" ++ ++ tag "UNTAR" + + test("Single-end") { + + +--- modules/nf-core/sratools/fasterqdump/tests/tags.yml ++++ /dev/null +@@ -1,2 +0,0 @@ +-sratools/fasterqdump: +- - modules/nf-core/sratools/fasterqdump/** + +************************************************************ From 7802ebc55aa05158f773e58608474901c183f6e9 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 30 Jan 2024 17:47:20 +0000 Subject: [PATCH 2/3] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1476a599..a91320c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #257](https://github.com/nf-core/fetchngs/pull/257) - Template update for nf-core/tools v2.12 - [PR #258](https://github.com/nf-core/fetchngs/pull/258) - Fixes for [PR #253](https://github.com/nf-core/fetchngs/pull/253) - [PR #259](https://github.com/nf-core/fetchngs/pull/259) - Add Aspera CLI download support to pipeline ([#68](https://github.com/nf-core/fetchngs/issues/68)) +- [PR #261](https://github.com/nf-core/fetchngs/pull/261) - Revert sratools fasterqdump version ([#221](https://github.com/nf-core/fetchngs/issues/221)) ### Software dependencies From 56a16a34e24843103d8b861eb8f6786ef5e05aac Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 30 Jan 2024 18:08:28 +0000 Subject: [PATCH 3/3] Update snapshots for new version of sratools --- .../fasterqdump/tests/main.nf.test.snap | 12 +++++------ .../tests/main.nf.test.snap | 20 +++++++++---------- 2 files changed, 16 insertions(+), 16 deletions(-) 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 e2cc2612..0e590311 100644 --- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap +++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ], "reads": [ [ @@ -24,11 +24,11 @@ ] ], "versions": [ - "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ] } ], - "timestamp": "2024-01-09T12:55:00.629261" + "timestamp": "2024-01-30T18:02:53.958171" }, "Paired-end": { "content": [ @@ -46,7 +46,7 @@ ] ], "1": [ - "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ], "reads": [ [ @@ -61,10 +61,10 @@ ] ], "versions": [ - "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ] } ], - "timestamp": "2024-01-09T12:55:34.40299" + "timestamp": "2024-01-30T18:03:20.841426" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap index 2123d3f7..63ba2e99 100644 --- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap @@ -3,7 +3,7 @@ "content": [ 19996 ], - "timestamp": "2024-01-11T11:52:21.464438219" + "timestamp": "2024-01-30T18:05:15.684489" }, "test_pe_reads_2_lines": { "content": [ @@ -16,29 +16,29 @@ "GTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACG" ] ], - "timestamp": "2024-01-11T11:52:21.437261931" + "timestamp": "2024-01-30T18:05:15.670447" }, "test_pe_reads_2_size": { "content": [ 2011460 ], - "timestamp": "2024-01-11T11:52:21.44875993" + "timestamp": "2024-01-30T18:05:15.675771" }, "versions": { "content": [ [ "versions.yml:md5,1a2218ff913fc33408bffccb081b5048", - "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224", - "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db" + "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d", + "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224" ] ], - "timestamp": "2024-01-11T12:11:06.731937323" + "timestamp": "2024-01-30T18:05:15.692165" }, "test_pe_reads_1_size": { "content": [ - 2011460 + 2013376 ], - "timestamp": "2024-01-11T11:52:21.428267242" + "timestamp": "2024-01-30T18:05:15.666916" }, "test_se_reads_lines": { "content": [ @@ -51,7 +51,7 @@ "ACGCAGGTGCCAGCAGCCGCGGTAATACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTTTTCAAGTCAGGGGTGGAAATACCCGGGGCCGTCAACCCGACCG" ] ], - "timestamp": "2024-01-11T11:52:21.45496474" + "timestamp": "2024-01-30T18:05:15.679779" }, "test_pe_reads_1_lines": { "content": [ @@ -64,6 +64,6 @@ "CGTACGAGCACGTCGCGAACCTGTAAAACAGGCAAACTGAGTTGGACGTGTGTTTTCTCGTTGAAACCAGGGACAAGGCTCTCCATCTTACCTTTCGGTCACACCCGGACGAAACCTAGATGTGCTGATGATCGGCTGCAACACGGACGAAACCGTAAGCAGCCTGCAGAAGATAGACGAGTTACTCGTGTCCTGTCAACGACAGTAATTAGTTATTAATTATACTGCGTGAGTGCAC" ] ], - "timestamp": "2024-01-11T11:52:21.400169604" + "timestamp": "2024-01-30T18:05:15.654112" } } \ No newline at end of file