diff --git a/modules.json b/modules.json index 6250d22..cb385c1 100644 --- a/modules.json +++ b/modules.json @@ -15,9 +15,14 @@ "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", "installed_by": ["modules"] }, + "sratools/fasterqdump": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, "sratools/prefetch": { "branch": "master", - "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } diff --git a/modules/local/sratools/fasterqdump/environment.yml b/modules/local/sratools/fasterqdump/environment.yml index 4011b69..dd0faa5 100644 --- a/modules/local/sratools/fasterqdump/environment.yml +++ b/modules/local/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/tests/data/ncbi_user_settings.mkfg b/tests/data/ncbi_user_settings.mkfg new file mode 100644 index 0000000..3c8df9f --- /dev/null +++ b/tests/data/ncbi_user_settings.mkfg @@ -0,0 +1,2 @@ +/LIBS/GUID = "5b0d4b7d-88c7-4802-98fd-e3afd06feb32" +/libs/cloud/report_instance_identity = "true" diff --git a/tests/modules/fasterqdump/main.nf.test b/tests/modules/fasterqdump/main.nf.test index 2ae17c3..52f3d11 100644 --- a/tests/modules/fasterqdump/main.nf.test +++ b/tests/modules/fasterqdump/main.nf.test @@ -12,7 +12,7 @@ nextflow_process { process { """ input[0] = Channel.of([ [irida_id: "SAMPLE1"], file("$baseDir/tests/data/ERR1109373.sra", checkIfExists: true) ]) - input[1] = [] + input[1] = file('$baseDir/tests/data/ncbi_user_settings.mkfg', checkIfExists: true) input[2] = [] """ } diff --git a/tests/modules/fasterqdump/main.nf.test.snap b/tests/modules/fasterqdump/main.nf.test.snap index 0bea139..8399ab9 100644 --- a/tests/modules/fasterqdump/main.nf.test.snap +++ b/tests/modules/fasterqdump/main.nf.test.snap @@ -15,7 +15,7 @@ ] ], "1": [ - "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ], "reads": [ [ @@ -30,7 +30,7 @@ ] ], "versions": [ - "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a" + "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295" ] } ], @@ -38,6 +38,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-31T11:23:17.630455595" + "timestamp": "2024-11-11T20:36:55.563890217" } } \ No newline at end of file diff --git a/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap b/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap index 566f55d..d51d6dd 100644 --- a/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap +++ b/tests/workflows/fastq_download_prefetch_fasterqdump_sratools/main.nf.test.snap @@ -24,8 +24,8 @@ ], "1": [ "versions.yml:md5,1a2218ff913fc33408bffccb081b5048", - "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224", - "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db" + "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d", + "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3" ], "reads": [ [ @@ -49,8 +49,8 @@ ], "versions": [ "versions.yml:md5,1a2218ff913fc33408bffccb081b5048", - "versions.yml:md5,98d78bba9f3da39a0b7db6e9c7dcc224", - "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db" + "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d", + "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3" ] } ], @@ -58,6 +58,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-11-05T15:53:20.740235848" + "timestamp": "2024-11-11T20:52:02.578591475" } } \ No newline at end of file