diff --git a/modules.json b/modules.json index 75a7c2a..53b2ccc 100644 --- a/modules.json +++ b/modules.json @@ -12,12 +12,12 @@ }, "blast/makeblastdb": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "a01c66c96e0bc610ad126e7adc4a94cd4acd1b48", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "d086322563bdbb08c94bf15a7db58a39ccdb1520", + "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56", "installed_by": ["modules"] }, "fastqc": { diff --git a/modules/local/filter.nf b/modules/local/filter.nf index 7f2e9ea..8016eda 100644 --- a/modules/local/filter.nf +++ b/modules/local/filter.nf @@ -2,10 +2,10 @@ process FILTER { tag "$meta.id" label 'process_high' - conda "bioconda::seqkit=2.6.0" + conda "bioconda::seqkit=2.7.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqkit%3A2.6.0--h9ee0642_0': - 'biocontainers/seqkit:2.6.0--h9ee0642_0'}" + 'https://depot.galaxyproject.org/singularity/seqkit:2.7.0--h9ee0642_0': + 'biocontainers/seqkit:2.7.0--h9ee0642_0'}" input: tuple val(meta), path(fastq), path(ids_to_remove) diff --git a/modules/local/prepare_fasta4blastn.nf b/modules/local/prepare_fasta4blastn.nf index b38a01e..39ce069 100644 --- a/modules/local/prepare_fasta4blastn.nf +++ b/modules/local/prepare_fasta4blastn.nf @@ -2,10 +2,10 @@ process PREPARE_FASTA4BLASTN { tag "$meta.id" label 'process_single' - conda "bioconda::seqkit=2.6.0" + conda "bioconda::seqkit=2.7.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqkit%3A2.6.0--h9ee0642_0': - 'biocontainers/seqkit:2.6.0--h9ee0642_0'}" + 'https://depot.galaxyproject.org/singularity/seqkit:2.7.0--h9ee0642_0': + 'biocontainers/seqkit:2.7.0--h9ee0642_0'}" input: tuple val(meta), path(trimmedreads), path(kraken2results) diff --git a/modules/nf-core/blast/makeblastdb/environment.yml b/modules/nf-core/blast/makeblastdb/environment.yml index cf84a60..a20783b 100644 --- a/modules/nf-core/blast/makeblastdb/environment.yml +++ b/modules/nf-core/blast/makeblastdb/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::blast=2.14.1 + - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf index cd1083d..a2c7318 100644 --- a/modules/nf-core/blast/makeblastdb/main.nf +++ b/modules/nf-core/blast/makeblastdb/main.nf @@ -4,8 +4,8 @@ process BLAST_MAKEBLASTDB { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0': - 'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }" + 'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1': + 'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test index 17dce8a..9b3f9a3 100644 --- a/modules/nf-core/fastp/tests/main.nf.test +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -19,11 +19,10 @@ nextflow_process { save_trimmed_fail = false save_merged = false - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] - + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -68,9 +67,9 @@ nextflow_process { process.out.reads_fail.collect { file(it[1]).getName() } + process.out.reads_merged.collect { file(it[1]).getName() } ).sort() - ).match("test_fastp_single_end-for_stub_match") + ).match("test_fastp_single_end-_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_single_end") } ) } } @@ -89,11 +88,10 @@ nextflow_process { save_trimmed_fail = false save_merged = false - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] - + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -118,7 +116,7 @@ nextflow_process { ).sort() ).match("test_fastp_single_end-for_stub_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_single_end_stub") } ) } } @@ -135,12 +133,11 @@ nextflow_process { save_trimmed_fail = false save_merged = false - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] - + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -199,9 +196,9 @@ nextflow_process { process.out.reads_fail.collect { file(it[1]).getName() } + process.out.reads_merged.collect { file(it[1]).getName() } ).sort() - ).match("test_fastp_paired_end-for_stub_match") + ).match("test_fastp_paired_end_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_paired_end") } ) } } @@ -220,12 +217,11 @@ nextflow_process { save_trimmed_fail = false save_merged = false - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] - + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -249,7 +245,7 @@ nextflow_process { ).sort() ).match("test_fastp_paired_end-for_stub_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_paired_end-stub") } ) } } @@ -266,10 +262,10 @@ nextflow_process { save_trimmed_fail = false save_merged = false - input[0] = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ] - ] - + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -314,9 +310,9 @@ nextflow_process { process.out.reads_fail.collect { file(it[1]).getName() } + process.out.reads_merged.collect { file(it[1]).getName() } ).sort() - ).match("test_fastp_interleaved-for_stub_match") + ).match("test_fastp_interleaved-_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_interleaved") } ) } } @@ -336,10 +332,10 @@ nextflow_process { save_trimmed_fail = false save_merged = false - input[0] = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ] - ] - + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -363,7 +359,7 @@ nextflow_process { ).sort() ).match("test_fastp_interleaved-for_stub_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_interleaved-stub") } ) } } @@ -380,9 +376,10 @@ nextflow_process { save_trimmed_fail = true save_merged = false - input[0] = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -423,7 +420,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } } }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_single_end_trim_fail") } ) } } @@ -440,13 +437,11 @@ nextflow_process { save_trimmed_fail = true save_merged = false - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -503,7 +498,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } } }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_paired_end_trim_fail") } ) } } @@ -519,11 +514,11 @@ nextflow_process { adapter_fasta = [] save_trimmed_fail = false save_merged = true - - input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -592,9 +587,9 @@ nextflow_process { process.out.reads_fail.collect { file(it[1]).getName() } + process.out.reads_merged.collect { file(it[1]).getName() } ).sort() - ).match("test_fastp_paired_end_merged-for_stub_match") + ).match("test_fastp_paired_end_merged_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_paired_end_merged") } ) } } @@ -613,10 +608,11 @@ nextflow_process { save_trimmed_fail = false save_merged = true - input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -640,7 +636,7 @@ nextflow_process { ).sort() ).match("test_fastp_paired_end_merged-for_stub_match") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_paired_end_merged_stub") } ) } } @@ -653,14 +649,15 @@ nextflow_process { } process { """ - adapter_fasta = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta", checkIfExists: true) + adapter_fasta = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ]) save_trimmed_fail = false save_merged = true - input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = adapter_fasta input[2] = save_trimmed_fail input[3] = save_merged @@ -719,7 +716,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } } }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("versions_paired_end_merged_adapterlist") } ) } } diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap index 1b7d241..b4c0e1d 100644 --- a/modules/nf-core/fastp/tests/main.nf.test.snap +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -1,5 +1,23 @@ { - "test_fastp_paired_end-for_stub_match": { + "fastp test_fastp_interleaved_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,168f516f7bd4b7b6c32da7cba87299a4" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:08:06.123035" + }, + "test_fastp_paired_end_merged-for_stub_match": { "content": [ [ [ @@ -9,12 +27,29 @@ "test.fastp.html", "test.fastp.json", "test.fastp.log", + "test.merged.fastq.gz", "{id=test, single_end=false}" ] ], - "timestamp": "2023-12-21T09:44:37.202512" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:10:13.467574" }, - "fastp test_fastp_interleaved_json": { + "versions_interleaved": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:56:24.615634793" + }, + "test_fastp_single_end_json": { "content": [ [ [ @@ -22,13 +57,64 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,168f516f7bd4b7b6c32da7cba87299a4" + "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" ] ] ], - "timestamp": "2023-10-17T11:04:45.794175881" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:06:00.223817" }, - "test_fastp_paired_end_merged-for_stub_match": { + "versions_paired_end": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:55:42.333545689" + }, + "test_fastp_paired_end_match": { + "content": [ + [ + [ + "test_1.fastp.fastq.gz", + "test_2.fastp.fastq.gz" + ], + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "{id=test, single_end=false}" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T12:03:06.431833729" + }, + "test_fastp_interleaved-_match": { + "content": [ + [ + "test.fastp.fastq.gz", + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "{id=test, single_end=true}" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T12:03:37.827323085" + }, + "test_fastp_paired_end_merged_match": { "content": [ [ [ @@ -42,29 +128,102 @@ "{id=test, single_end=false}" ] ], - "timestamp": "2023-12-21T09:53:45.237014" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T12:08:44.496251446" }, - "test_fastp_single_end_json": { + "versions_single_end_stub": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:55:27.354051299" + }, + "versions_interleaved-stub": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:56:46.535528418" + }, + "versions_single_end_trim_fail": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:59:03.724591407" + }, + "test_fastp_paired_end-for_stub_match": { "content": [ [ [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" - ] + "test_1.fastp.fastq.gz", + "test_2.fastp.fastq.gz" + ], + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "{id=test, single_end=false}" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:07:15.398827" + }, + "versions_paired_end-stub": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:56:06.50017282" + }, + "versions_single_end": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" ] ], - "timestamp": "2023-10-17T11:04:10.566343705" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:55:07.67921647" }, - "versions": { + "versions_paired_end_merged_stub": { "content": [ [ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" ] ], - "timestamp": "2023-10-17T11:04:10.582076024" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:59:47.350653154" }, "test_fastp_interleaved-for_stub_match": { "content": [ @@ -76,7 +235,23 @@ "{id=test, single_end=true}" ] ], - "timestamp": "2023-12-21T09:48:43.148485" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:08:06.127974" + }, + "versions_paired_end_trim_fail": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:59:18.140484878" }, "test_fastp_single_end-for_stub_match": { "content": [ @@ -88,7 +263,51 @@ "{id=test, single_end=true}" ] ], - "timestamp": "2023-12-21T09:20:07.254788" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:06:00.244202" + }, + "test_fastp_single_end-_match": { + "content": [ + [ + "test.fastp.fastq.gz", + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "{id=test, single_end=true}" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:57:30.791982648" + }, + "versions_paired_end_merged_adapterlist": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T12:05:37.845370554" + }, + "versions_paired_end_merged": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-01T11:59:32.860543858" }, "test_fastp_single_end_trim_fail_json": { "content": [ @@ -102,6 +321,10 @@ ] ] ], - "timestamp": "2023-10-17T11:05:00.379878948" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T18:08:41.942317" } } \ No newline at end of file