diff --git a/modules/nf-core/isoseq3/refine/environment.yml b/modules/nf-core/isoseq/cluster/environment.yml similarity index 57% rename from modules/nf-core/isoseq3/refine/environment.yml rename to modules/nf-core/isoseq/cluster/environment.yml index 5061bac0f28..bb5355772c6 100644 --- a/modules/nf-core/isoseq3/refine/environment.yml +++ b/modules/nf-core/isoseq/cluster/environment.yml @@ -1,7 +1,7 @@ -name: isoseq3_refine +name: isoseq_cluster channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::isoseq3=3.8.2 + - bioconda::isoseq=4.0.0 diff --git a/modules/nf-core/isoseq3/cluster/main.nf b/modules/nf-core/isoseq/cluster/main.nf similarity index 67% rename from modules/nf-core/isoseq3/cluster/main.nf rename to modules/nf-core/isoseq/cluster/main.nf index fd06a696aa6..d83249d5f89 100644 --- a/modules/nf-core/isoseq3/cluster/main.nf +++ b/modules/nf-core/isoseq/cluster/main.nf @@ -1,11 +1,11 @@ -process ISOSEQ3_CLUSTER { +process ISOSEQ_CLUSTER { tag "$meta.id" label 'process_medium' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/isoseq3:3.8.1--h9ee0642_0' : - 'biocontainers/isoseq3:3.8.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/isoseq:4.0.0--h9ee0642_0' : + 'biocontainers/isoseq:4.0.0--h9ee0642_0' }" input: tuple val(meta), path(bam) @@ -31,7 +31,7 @@ process ISOSEQ3_CLUSTER { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - isoseq3 \\ + isoseq \\ cluster \\ $bam \\ ${prefix}.transcripts.bam \\ @@ -39,7 +39,23 @@ process ISOSEQ3_CLUSTER { cat <<-END_VERSIONS > versions.yml "${task.process}": - isoseq3: \$( isoseq3 cluster --version | head -n 1 | sed 's/isoseq cluster //g' | sed 's/ (.*//g' ) + isoseq: \$( isoseq cluster --version | head -n 1 | sed 's/isoseq cluster //g' | sed 's/ (.*//g' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch dummy.transcripts.bam + touch dummy.transcripts.bam.pbi + touch dummy.transcripts.cluster + touch dummy.transcripts.cluster_report.csv + touch dummy.transcripts.transcriptset.xml + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + isoseq: \$( isoseq cluster --version | head -n 1 | sed 's/isoseq cluster //g' | sed 's/ (.*//g' ) END_VERSIONS """ } diff --git a/modules/nf-core/isoseq3/cluster/meta.yml b/modules/nf-core/isoseq/cluster/meta.yml similarity index 89% rename from modules/nf-core/isoseq3/cluster/meta.yml rename to modules/nf-core/isoseq/cluster/meta.yml index 6089116fb3a..a7879668dde 100644 --- a/modules/nf-core/isoseq3/cluster/meta.yml +++ b/modules/nf-core/isoseq/cluster/meta.yml @@ -1,10 +1,13 @@ -name: isoseq3_cluster -description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences +name: isoseq_cluster +description: IsoSeq - Cluster - Cluster trimmed consensus sequences keywords: - cluster + - HiFi + - isoseq + - Pacbio tools: - - isoseq3: - description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences + - isoseq: + description: IsoSeq - Cluster - Cluster trimmed consensus sequences homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md @@ -17,7 +20,7 @@ input: e.g. [ id:'test' ] - bam: type: file - description: BAM file generated by isoseq3 refine + description: BAM file generated by isoseq refine pattern: "*.bam" output: - meta: @@ -25,7 +28,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - version: + - versions: type: file description: File containing software version pattern: "versions.yml" diff --git a/modules/nf-core/isoseq/cluster/tests/main.nf.test b/modules/nf-core/isoseq/cluster/tests/main.nf.test new file mode 100644 index 00000000000..32295fd66a5 --- /dev/null +++ b/modules/nf-core/isoseq/cluster/tests/main.nf.test @@ -0,0 +1,66 @@ +nextflow_process { + + name "Test Process ISOSEQ_CLUSTER" + script "../main.nf" + config "./nextflow.config" + process "ISOSEQ_CLUSTER" + + tag "modules" + tag "modules_nfcore" + tag "isoseq" + tag "isoseq/cluster" + + test("PacBio isoseq cluster - CCS clustering test") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.bam).match("bam") }, + { assert snapshot(process.out.pbi).match("pbi") }, + { assert snapshot(process.out.cluster).match("cluster") }, + { assert snapshot(process.out.cluster_report).match("cluster_report") }, + { assert snapshot(process.out.hq_bam).match("hq_bam") }, + { assert snapshot(process.out.hq_pbi).match("hq_pbi") }, + { assert snapshot(process.out.lq_bam).match("lq_bam") }, + { assert snapshot(process.out.lq_pbi).match("lq_pbi") }, + { assert snapshot(process.out.singletons_bam).match("singletons_bam") }, + { assert snapshot(process.out.singletons_pbi).match("singletons_pbi") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("PacBio isoseq cluster - CCS clustering test - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/isoseq/cluster/tests/main.nf.test.snap b/modules/nf-core/isoseq/cluster/tests/main.nf.test.snap new file mode 100644 index 00000000000..fd00addd367 --- /dev/null +++ b/modules/nf-core/isoseq/cluster/tests/main.nf.test.snap @@ -0,0 +1,317 @@ +{ + "PacBio isoseq cluster - CCS clustering test - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.transcripts.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.transcripts.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + + ], + "11": [ + "versions.yml:md5,f6ca1e932945375fac827c468c60ef2a" + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.transcripts.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "dummy.transcripts.cluster_report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "dummy.transcripts.transcriptset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + [ + { + "id": "test" + }, + "dummy.transcripts.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cluster": [ + [ + { + "id": "test" + }, + "dummy.transcripts.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cluster_report": [ + [ + { + "id": "test" + }, + "dummy.transcripts.cluster_report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "hq_bam": [ + + ], + "hq_pbi": [ + + ], + "lq_bam": [ + + ], + "lq_pbi": [ + + ], + "pbi": [ + [ + { + "id": "test" + }, + "dummy.transcripts.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "singletons_bam": [ + + ], + "singletons_pbi": [ + + ], + "transcriptset": [ + [ + { + "id": "test" + }, + "dummy.transcripts.transcriptset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f6ca1e932945375fac827c468c60ef2a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:56:41.744477" + }, + "cluster": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.cluster:md5,e25f5e4179bc8b6accec024008001c52" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-16T17:51:37.025827" + }, + "singletons_bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.singletons.bam:md5,f8bcaa7d071be24c199d4243e77a65a6" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:36.093361" + }, + "lq_bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.lq.bam:md5,f4948859ae09db09221ef7c08b9dc1ea" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:36.011969" + }, + "hq_bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.hq.bam:md5,0ad13a6f56aa1800cc553ee3e8f52e59" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:35.949396" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,f6ca1e932945375fac827c468c60ef2a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-23T10:04:24.098063" + }, + "pbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.bam.pbi:md5,0f9569d3132bc58a3b6827364215d2a8" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:35.917491" + }, + "singletons_pbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.singletons.bam.pbi:md5,f63eed07e30bc66a72c6ebd24d0116e0" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:36.151147" + }, + "cluster_report": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.cluster_report.csv:md5,5437fc2d59122b28d81c3f1215f6ff17" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-16T17:51:37.069648" + }, + "hq_pbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.hq.bam.pbi:md5,4eecd253bb8cb0dbdc039ec80bb88ba0" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:35.977037" + }, + "lq_pbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.lq.bam.pbi:md5,d1f96a5748c71d9eb1b69c620412c863" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:36.032895" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.transcripts.bam:md5,540c126bca7bd75f7a9084d3e2e642f7" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T08:55:35.880903" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/pbccs/nextflow.config b/modules/nf-core/isoseq/cluster/tests/nextflow.config similarity index 65% rename from tests/modules/nf-core/pbccs/nextflow.config rename to modules/nf-core/isoseq/cluster/tests/nextflow.config index 869909cea3e..f3e01da355b 100644 --- a/tests/modules/nf-core/pbccs/nextflow.config +++ b/modules/nf-core/isoseq/cluster/tests/nextflow.config @@ -1,9 +1,6 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: PBCCS { - ext.args = '--min-rq 0.9' - } + ext.args = '--singletons --use-qvs --verbose' } diff --git a/modules/nf-core/isoseq/cluster/tests/tags.yml b/modules/nf-core/isoseq/cluster/tests/tags.yml new file mode 100644 index 00000000000..19efe2add7d --- /dev/null +++ b/modules/nf-core/isoseq/cluster/tests/tags.yml @@ -0,0 +1,2 @@ +isoseq/cluster: + - modules/nf-core/isoseq/cluster/** diff --git a/modules/nf-core/isoseq3/cluster/environment.yml b/modules/nf-core/isoseq/refine/environment.yml similarity index 56% rename from modules/nf-core/isoseq3/cluster/environment.yml rename to modules/nf-core/isoseq/refine/environment.yml index 957e456c0b6..05fb46ff5e4 100644 --- a/modules/nf-core/isoseq3/cluster/environment.yml +++ b/modules/nf-core/isoseq/refine/environment.yml @@ -1,7 +1,7 @@ -name: isoseq3_cluster +name: isoseq_refine channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::isoseq3=3.8.1 + - bioconda::isoseq=4.0.0 diff --git a/modules/nf-core/isoseq/refine/main.nf b/modules/nf-core/isoseq/refine/main.nf new file mode 100644 index 00000000000..63bcf5ef6a8 --- /dev/null +++ b/modules/nf-core/isoseq/refine/main.nf @@ -0,0 +1,58 @@ +process ISOSEQ_REFINE { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/isoseq:4.0.0--h9ee0642_0' : + 'biocontainers/isoseq:4.0.0--h9ee0642_0' }" + + input: + tuple val(meta), path(bam) + path primers + + output: + tuple val(meta), path("*.bam") , emit: bam + tuple val(meta), path("*.bam.pbi") , emit: pbi + tuple val(meta), path("*.consensusreadset.xml") , emit: consensusreadset + tuple val(meta), path("*.filter_summary.report.json"), emit: summary + tuple val(meta), path("*.report.csv") , emit: report + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + isoseq \\ + refine \\ + -j $task.cpus \\ + $args \\ + $bam \\ + $primers \\ + ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + isoseq: \$( isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch dummy.bam + touch dummy.bam.pbi + touch dummy.consensusreadset.xml + touch dummy.filter_summary.report.json + touch dummy.report.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + isoseq: \$( isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/isoseq3/refine/meta.yml b/modules/nf-core/isoseq/refine/meta.yml similarity index 94% rename from modules/nf-core/isoseq3/refine/meta.yml rename to modules/nf-core/isoseq/refine/meta.yml index 3f8d8b95373..40f6c4b0f0a 100644 --- a/modules/nf-core/isoseq3/refine/meta.yml +++ b/modules/nf-core/isoseq/refine/meta.yml @@ -1,4 +1,4 @@ -name: isoseq3_refine +name: isoseq_refine description: Remove polyA tail and artificial concatemers keywords: - isoseq @@ -7,8 +7,8 @@ keywords: - pacbio - polyA_tail tools: - - isoseq3: - description: IsoSeq3 - Scalable De Novo Isoform Discovery + - isoseq: + description: IsoSeq - Scalable De Novo Isoform Discovery homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md diff --git a/modules/nf-core/isoseq/refine/tests/main.nf.test b/modules/nf-core/isoseq/refine/tests/main.nf.test new file mode 100644 index 00000000000..b1c7dda6191 --- /dev/null +++ b/modules/nf-core/isoseq/refine/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process ISOSEQ_REFINE" + script "../main.nf" + config "./nextflow.config" + process "ISOSEQ_REFINE" + + tag "modules" + tag "modules_nfcore" + tag "isoseq" + tag "isoseq/refine" + + test("PacBio isoseq refine - Chimeras Removing test") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.bam).match("bam") }, + { assert snapshot(process.out.pbi).match("pbi") }, + { assert path(process.out.consensusreadset.get(0).get(1)).text.contains("PacBio.DataSet.ConsensusReadSet") }, + { assert path(process.out.summary.get(0).get(1)).text.contains("pbcopper") }, + { assert snapshot(process.out.report).match("report") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("PacBio isoseq refine - Chimeras Removing test - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/isoseq/refine/tests/main.nf.test.snap b/modules/nf-core/isoseq/refine/tests/main.nf.test.snap new file mode 100644 index 00000000000..62da6305625 --- /dev/null +++ b/modules/nf-core/isoseq/refine/tests/main.nf.test.snap @@ -0,0 +1,162 @@ +{ + "PacBio isoseq refine - Chimeras Removing test - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.consensusreadset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "dummy.filter_summary.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "dummy.report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,277ea2c8a1f4592efee1f336dfdd32e5" + ], + "bam": [ + [ + { + "id": "test" + }, + "dummy.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "consensusreadset": [ + [ + { + "id": "test" + }, + "dummy.consensusreadset.xml:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pbi": [ + [ + { + "id": "test" + }, + "dummy.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "dummy.report.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "dummy.filter_summary.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,277ea2c8a1f4592efee1f336dfdd32e5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T22:41:31.59497" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,277ea2c8a1f4592efee1f336dfdd32e5" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-14T10:40:47.708497" + }, + "pbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.refine.bam.pbi:md5,fcd3c9b9c7efea71732591ff1271a3b5" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-14T10:34:21.23301" + }, + "report": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.refine.report.csv:md5,d42a139e5d9b08396bdb087c01243ea9" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-14T10:34:21.292332" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.refine.bam:md5,4a666931c2c8843d8a8f0d901e1ba15f" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-14T10:34:21.174269" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/isoseq3/refine/nextflow.config b/modules/nf-core/isoseq/refine/tests/nextflow.config similarity index 58% rename from tests/modules/nf-core/isoseq3/refine/nextflow.config rename to modules/nf-core/isoseq/refine/tests/nextflow.config index 6a4dea9f972..3c49ec74103 100644 --- a/tests/modules/nf-core/isoseq3/refine/nextflow.config +++ b/modules/nf-core/isoseq/refine/tests/nextflow.config @@ -1,9 +1,6 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ISOSEQ3_REFINE { - ext.prefix = { "${meta.id}.refine" } - } + ext.prefix = { "${meta.id}.refine" } } diff --git a/modules/nf-core/isoseq/refine/tests/tags.yml b/modules/nf-core/isoseq/refine/tests/tags.yml new file mode 100644 index 00000000000..c6f3ffb6a2a --- /dev/null +++ b/modules/nf-core/isoseq/refine/tests/tags.yml @@ -0,0 +1,2 @@ +isoseq/refine: + - modules/nf-core/isoseq/refine/** diff --git a/modules/nf-core/isoseq3/refine/main.nf b/modules/nf-core/isoseq3/refine/main.nf deleted file mode 100644 index 79f8df4fed4..00000000000 --- a/modules/nf-core/isoseq3/refine/main.nf +++ /dev/null @@ -1,42 +0,0 @@ -process ISOSEQ3_REFINE { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/isoseq3:3.8.2--h9ee0642_0' : - 'biocontainers/isoseq3:3.8.2--h9ee0642_0' }" - - input: - tuple val(meta), path(bam) - path primers - - output: - tuple val(meta), path("*.bam") , emit: bam - tuple val(meta), path("*.bam.pbi") , emit: pbi - tuple val(meta), path("*.consensusreadset.xml") , emit: consensusreadset - tuple val(meta), path("*.filter_summary.report.json") , emit: summary - tuple val(meta), path("*.report.csv") , emit: report - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - isoseq3 \\ - refine \\ - -j $task.cpus \\ - $args \\ - $bam \\ - $primers \\ - ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - isoseq3: \$( isoseq3 refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\\+//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/lima/environment.yml b/modules/nf-core/lima/environment.yml index 0e1d7e9634a..a9718bc190d 100644 --- a/modules/nf-core/lima/environment.yml +++ b/modules/nf-core/lima/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::lima=2.7.1 + - bioconda::lima=2.9.0 diff --git a/modules/nf-core/lima/main.nf b/modules/nf-core/lima/main.nf index 94023b9b399..e44fdda5c3c 100644 --- a/modules/nf-core/lima/main.nf +++ b/modules/nf-core/lima/main.nf @@ -4,8 +4,8 @@ process LIMA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/lima:2.7.1--h9ee0642_0' : - 'biocontainers/lima:2.7.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/lima:2.9.0--h9ee0642_1' : + 'biocontainers/lima:2.9.0--h9ee0642_1' }" input: tuple val(meta), path(ccs) @@ -67,4 +67,18 @@ process LIMA { lima: \$( lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g' ) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch dummy.counts + touch dummy.report + touch dummy.summary + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + lima: \$( lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\\+//g' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/lima/meta.yml b/modules/nf-core/lima/meta.yml index 9077120044c..ad4ebbfa0c5 100644 --- a/modules/nf-core/lima/meta.yml +++ b/modules/nf-core/lima/meta.yml @@ -69,6 +69,22 @@ output: type: file description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered. pattern: "*.summary" + - fasta: + type: file + description: A fasta file of ccs purged of primers. + pattern: "*.fa" + - fastagz: + type: file + description: A fasta.gz file of ccs purged of primers. + pattern: "*.fasta.gz" + - fastq: + type: file + description: A fastq file of ccs purged of primers. + pattern: "*.fastq" + - fastqgz: + type: file + description: A fastq.gz file of ccs purged of primers. + pattern: "*.fastq.gz" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/lima/tests/main.nf.test b/modules/nf-core/lima/tests/main.nf.test new file mode 100644 index 00000000000..b2cdeb47881 --- /dev/null +++ b/modules/nf-core/lima/tests/main.nf.test @@ -0,0 +1,263 @@ +nextflow_process { + + name "Test Process LIMA" + script "../main.nf" + config "./nextflow.config" + process "LIMA" + + tag "modules" + tag "modules_nfcore" + tag "lima" + + test("LIMA - Primer Removal - Input => bam") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.bam', checkIfExists: true), + ] + input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts).match("counts") }, + { assert snapshot(process.out.report).match("report") }, + { assert snapshot(process.out.summary).match("summary") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(process.out.bam).match("bam") }, + { assert snapshot(process.out.pbi).match("pbi") }, + { assert snapshot(process.out.fasta).match("fasta") }, + { assert snapshot(process.out.fastagz).match("fastagz") }, + { assert snapshot(process.out.fastq).match("fastq") }, + { assert snapshot(process.out.fastqgz).match("fastqgz") }, + { assert snapshot(process.out.clips).match("clips") }, + { assert snapshot(process.out.guess).match("guess") } + ) + } + + } + + test("LIMA - Primer Removal - Input => fa") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fa.gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fq") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fq.gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.ccs.bam', checkIfExists: true), + ] + input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fa - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fa.gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fq - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("LIMA - Primer Removal - Input => fq.gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true), + ] + input[1] = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/lima/tests/main.nf.test.snap b/modules/nf-core/lima/tests/main.nf.test.snap new file mode 100644 index 00000000000..f64e3dc6521 --- /dev/null +++ b/modules/nf-core/lima/tests/main.nf.test.snap @@ -0,0 +1,1486 @@ +{ + "fastqgz": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:01.98256" + }, + "counts": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,842c6a23ca2de504ced4538ad5111da1" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:00.491188" + }, + "clips": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,fa03bc75bd78b2648a139fd67c69208f" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:02.19417" + }, + "LIMA - Primer Removal - Input => fq.gz - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + + ], + "13": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + + ], + "clips": [ + + ], + "counts": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + + ], + "json": [ + + ], + "pbi": [ + + ], + "report": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:43.376049" + }, + "LIMA - Primer Removal - Input => fq.gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,767b687e6eda7b24cd0e577f527eb2f0" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,ad2a9b1eeb4cda4a1f69ef4b7520b5fd" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,5c16ef8122f6f1798acc30eb8a30828c" + ] + ], + "13": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,31b988aab6bda84867e704b9edd8a763" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,e91d3c386aaf4effa63f33ee2eb7da2a" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz:md5,ef395f689c5566f501e300bb83d7a5f2" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "clips": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,5c16ef8122f6f1798acc30eb8a30828c" + ] + ], + "counts": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,767b687e6eda7b24cd0e577f527eb2f0" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz:md5,ef395f689c5566f501e300bb83d7a5f2" + ] + ], + "guess": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,31b988aab6bda84867e704b9edd8a763" + ] + ], + "json": [ + + ], + "pbi": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,ad2a9b1eeb4cda4a1f69ef4b7520b5fd" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,e91d3c386aaf4effa63f33ee2eb7da2a" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:13.306885" + }, + "LIMA - Primer Removal - Input => fq": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,767b687e6eda7b24cd0e577f527eb2f0" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,ad2a9b1eeb4cda4a1f69ef4b7520b5fd" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,5c16ef8122f6f1798acc30eb8a30828c" + ] + ], + "13": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,31b988aab6bda84867e704b9edd8a763" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,e91d3c386aaf4effa63f33ee2eb7da2a" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fastq:md5,ef395f689c5566f501e300bb83d7a5f2" + ] + ], + "9": [ + + ], + "bam": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "clips": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,5c16ef8122f6f1798acc30eb8a30828c" + ] + ], + "counts": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,767b687e6eda7b24cd0e577f527eb2f0" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.fastq:md5,ef395f689c5566f501e300bb83d7a5f2" + ] + ], + "fastqgz": [ + + ], + "guess": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,31b988aab6bda84867e704b9edd8a763" + ] + ], + "json": [ + + ], + "pbi": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,ad2a9b1eeb4cda4a1f69ef4b7520b5fd" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,e91d3c386aaf4effa63f33ee2eb7da2a" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:07.559264" + }, + "LIMA - Primer Removal - Input => fa.gz - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + + ], + "13": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + + ], + "clips": [ + + ], + "counts": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + + ], + "json": [ + + ], + "pbi": [ + + ], + "report": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:30.69067" + }, + "fasta": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:01.262691" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,d3de1934aa8fb39e961345916b3ae57b" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:00.822221" + }, + "fastq": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:01.752773" + }, + "summary": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,bcbcaaaca418bdeb91141c81715ca420" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:00.704932" + }, + "LIMA - Primer Removal - Input => fq - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + + ], + "13": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + + ], + "clips": [ + + ], + "counts": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + + ], + "json": [ + + ], + "pbi": [ + + ], + "report": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:37.019064" + }, + "LIMA - Primer Removal - Input => bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + + ], + "13": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + + ], + "clips": [ + + ], + "counts": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + + ], + "json": [ + + ], + "pbi": [ + + ], + "report": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:18.958286" + }, + "LIMA - Primer Removal - Input => fa - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + + ], + "13": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + + ], + "clips": [ + + ], + "counts": [ + [ + { + "id": "test" + }, + "dummy.counts:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + + ], + "json": [ + + ], + "pbi": [ + + ], + "report": [ + [ + { + "id": "test" + }, + "dummy.report:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "dummy.summary:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:25.020259" + }, + "fastagz": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:01.493258" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:00.76398" + }, + "guess": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,d3675af3ca8a908ee9e3c231668392d3" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:02.396472" + }, + "pbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,b531dcf8afc5f6c1caf40c7affb6a90c" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:01.042955" + }, + "report": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,dc073985322ae0a003ccc7e0fa4db5e6" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-17T11:35:00.626772" + }, + "LIMA - Primer Removal - Input => fa": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,a4ceaa408be334eaa711577e95f8730e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,bd4a8bde17471563cf91aab4c787911d" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,1012bc8874a14836f291bac48e8482a4" + ] + ], + "13": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,651e5f2b438b8ceadb3e06a2177e1818" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,03be2311ba4afb878d8e547ab38c11eb" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "clips": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,1012bc8874a14836f291bac48e8482a4" + ] + ], + "counts": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,a4ceaa408be334eaa711577e95f8730e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,651e5f2b438b8ceadb3e06a2177e1818" + ] + ], + "json": [ + + ], + "pbi": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,bd4a8bde17471563cf91aab4c787911d" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,03be2311ba4afb878d8e547ab38c11eb" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:46:54.854736" + }, + "LIMA - Primer Removal - Input => fa.gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,a4ceaa408be334eaa711577e95f8730e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,bd4a8bde17471563cf91aab4c787911d" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,1012bc8874a14836f291bac48e8482a4" + ] + ], + "13": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,651e5f2b438b8ceadb3e06a2177e1818" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,03be2311ba4afb878d8e547ab38c11eb" + ] + ], + "3": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "4": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "bam": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam:md5,c5d3d376ca7ffc32ef5cbabcc9850804" + ] + ], + "clips": [ + [ + { + "id": "test" + }, + "test.fl.lima.clips:md5,1012bc8874a14836f291bac48e8482a4" + ] + ], + "counts": [ + [ + { + "id": "test" + }, + "test.fl.lima.counts:md5,a4ceaa408be334eaa711577e95f8730e" + ] + ], + "fasta": [ + + ], + "fastagz": [ + + ], + "fastq": [ + + ], + "fastqgz": [ + + ], + "guess": [ + [ + { + "id": "test" + }, + "test.fl.lima.guess:md5,651e5f2b438b8ceadb3e06a2177e1818" + ] + ], + "json": [ + + ], + "pbi": [ + [ + { + "id": "test" + }, + "test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi:md5,d1d6a2f961b9fb3d29837555706c59eb" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test.fl.lima.report:md5,bd4a8bde17471563cf91aab4c787911d" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.fl.lima.summary:md5,03be2311ba4afb878d8e547ab38c11eb" + ] + ], + "versions": [ + "versions.yml:md5,1a47b30bece32a2fcd9a70f9356dc30d" + ], + "xml": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:47:01.506833" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/isoseq3/cluster/nextflow.config b/modules/nf-core/lima/tests/nextflow.config similarity index 56% rename from tests/modules/nf-core/isoseq3/cluster/nextflow.config rename to modules/nf-core/lima/tests/nextflow.config index 8bfeaebdcc5..ac259b70cb6 100644 --- a/tests/modules/nf-core/isoseq3/cluster/nextflow.config +++ b/modules/nf-core/lima/tests/nextflow.config @@ -1,9 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ISOSEQ3_CLUSTER { - ext.args = '--singletons --use-qvs --verbose' - } + ext.args = '--isoseq --peek-guess' + ext.prefix = { "${meta.id}.fl" } } diff --git a/modules/nf-core/lima/tests/tags.yml b/modules/nf-core/lima/tests/tags.yml new file mode 100644 index 00000000000..bf24adddf80 --- /dev/null +++ b/modules/nf-core/lima/tests/tags.yml @@ -0,0 +1,2 @@ +lima: + - modules/nf-core/lima/** diff --git a/modules/nf-core/pbccs/main.nf b/modules/nf-core/pbccs/main.nf index 871a14926ee..dd2d0ad0182 100644 --- a/modules/nf-core/pbccs/main.nf +++ b/modules/nf-core/pbccs/main.nf @@ -42,4 +42,21 @@ process PBCCS { pbccs: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch dummy.chunk1.bam + touch dummy.chunk1.bam.pbi + touch dummy.report.txt + touch dummy.report.json + echo "test" > dummy.metrics.json + gzip dummy.metrics.json + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbccs: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/pbccs/tests/main.nf.test b/modules/nf-core/pbccs/tests/main.nf.test new file mode 100644 index 00000000000..ef70d05833b --- /dev/null +++ b/modules/nf-core/pbccs/tests/main.nf.test @@ -0,0 +1,69 @@ +nextflow_process { + + name "Test Process PBCCS" + script "../main.nf" + config "./nextflow.config" + process "PBCCS" + + tag "modules" + tag "modules_nfcore" + tag "pbccs" + + test("PacBio pbccs - Compute CSS test") { + + when { + process { + """ + input[0] = [ + [ id:'alz' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true) + ] + input[1] = 2 + input[2] = 3 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.bam).match("bam") }, + { assert snapshot(process.out.pbi).match("pbi") }, + { assert snapshot(process.out.report_txt).match("report_txt") }, + { assert path(process.out.report_json.get(0).get(1)).text.contains("pbcopper") }, + { assert path(process.out.metrics.get(0).get(1)).linesGzip.get(0).toString().contains("zmws") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("PacBio pbccs - Compute CSS test - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'alz' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true) + ] + input[1] = 2 + input[2] = 3 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/pbccs/tests/main.nf.test.snap b/modules/nf-core/pbccs/tests/main.nf.test.snap new file mode 100644 index 00000000000..b47348c3001 --- /dev/null +++ b/modules/nf-core/pbccs/tests/main.nf.test.snap @@ -0,0 +1,162 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,391e95cf678a7992d6d3f3b437efc61a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T08:38:30.999138" + }, + "pbi": { + "content": [ + [ + [ + { + "id": "alz" + }, + "alz.chunk2.bam.pbi:md5,36c3d2843aae90739ee8ca82d27abd55" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T16:37:53.581983" + }, + "report_txt": { + "content": [ + [ + [ + { + "id": "alz" + }, + "alz.chunk2.report.txt:md5,67583febb144333e3f854c7bf4a17a50" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T16:37:53.600993" + }, + "PacBio pbccs - Compute CSS test - stub": { + "content": [ + { + "0": [ + [ + { + "id": "alz" + }, + "dummy.chunk1.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "alz" + }, + "dummy.chunk1.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "alz" + }, + "dummy.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "alz" + }, + "dummy.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "alz" + }, + "dummy.metrics.json.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + ] + ], + "5": [ + "versions.yml:md5,391e95cf678a7992d6d3f3b437efc61a" + ], + "bam": [ + [ + { + "id": "alz" + }, + "dummy.chunk1.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "alz" + }, + "dummy.metrics.json.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + ] + ], + "pbi": [ + [ + { + "id": "alz" + }, + "dummy.chunk1.bam.pbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_json": [ + [ + { + "id": "alz" + }, + "dummy.report.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report_txt": [ + [ + { + "id": "alz" + }, + "dummy.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,391e95cf678a7992d6d3f3b437efc61a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T10:24:03.471175" + }, + "bam": { + "content": [ + [ + [ + { + "id": "alz" + }, + "alz.chunk2.bam:md5,306ba0287e3c7f4cd8f5af577af7ac62" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-13T16:37:53.559407" + } +} \ No newline at end of file diff --git a/modules/nf-core/pbccs/tests/nextflow.config b/modules/nf-core/pbccs/tests/nextflow.config new file mode 100644 index 00000000000..2c2b4fef149 --- /dev/null +++ b/modules/nf-core/pbccs/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = '--min-rq 0.9' +} diff --git a/modules/nf-core/pbccs/tests/tags.yml b/modules/nf-core/pbccs/tests/tags.yml new file mode 100644 index 00000000000..602160632f2 --- /dev/null +++ b/modules/nf-core/pbccs/tests/tags.yml @@ -0,0 +1,2 @@ +pbccs: + - modules/nf-core/pbccs/** diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 7e346c4ef57..63338efbd3a 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -936,12 +936,6 @@ iphop/predict: ismapper: - modules/nf-core/ismapper/** - tests/modules/nf-core/ismapper/** -isoseq3/cluster: - - modules/nf-core/isoseq3/cluster/** - - tests/modules/nf-core/isoseq3/cluster/** -isoseq3/refine: - - modules/nf-core/isoseq3/refine/** - - tests/modules/nf-core/isoseq3/refine/** ivar/consensus: - modules/nf-core/ivar/consensus/** - tests/modules/nf-core/ivar/consensus/** @@ -1038,9 +1032,6 @@ leehom: legsta: - modules/nf-core/legsta/** - tests/modules/nf-core/legsta/** -lima: - - modules/nf-core/lima/** - - tests/modules/nf-core/lima/** limma/differential: - modules/nf-core/limma/differential/** - tests/modules/nf-core/limma/differential/** @@ -1371,9 +1362,6 @@ pasty: pbbam/pbmerge: - modules/nf-core/pbbam/pbmerge/** - tests/modules/nf-core/pbbam/pbmerge/** -pbccs: - - modules/nf-core/pbccs/** - - tests/modules/nf-core/pbccs/** pbptyper: - modules/nf-core/pbptyper/** - tests/modules/nf-core/pbptyper/** diff --git a/tests/modules/nf-core/isoseq3/cluster/main.nf b/tests/modules/nf-core/isoseq3/cluster/main.nf deleted file mode 100644 index 3f586d9a5f5..00000000000 --- a/tests/modules/nf-core/isoseq3/cluster/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ISOSEQ3_CLUSTER } from '../../../../../modules/nf-core/isoseq3/cluster/main.nf' - -workflow test_isoseq3_cluster { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['refine'], checkIfExists: true), - ] - - ISOSEQ3_CLUSTER ( input ) -} diff --git a/tests/modules/nf-core/isoseq3/cluster/test.yml b/tests/modules/nf-core/isoseq3/cluster/test.yml deleted file mode 100644 index 135bf124a15..00000000000 --- a/tests/modules/nf-core/isoseq3/cluster/test.yml +++ /dev/null @@ -1,28 +0,0 @@ -- name: isoseq3 cluster test_isoseq3_cluster - command: nextflow run ./tests/modules/nf-core/isoseq3/cluster -entry test_isoseq3_cluster -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/isoseq3/cluster/nextflow.config - tags: - - isoseq3/cluster - - isoseq3 - files: - - path: output/isoseq3/test.transcripts.bam - md5sum: fea0b7a45ef6e08f5af9bd4529dd113b - - path: output/isoseq3/test.transcripts.bam.pbi - md5sum: 0f9569d3132bc58a3b6827364215d2a8 - - path: output/isoseq3/test.transcripts.cluster - md5sum: e25f5e4179bc8b6accec024008001c52 - - path: output/isoseq3/test.transcripts.cluster_report.csv - md5sum: 5437fc2d59122b28d81c3f1215f6ff17 - - path: output/isoseq3/test.transcripts.hq.bam - md5sum: 0a5e2e7c82f9cc1d8d4bb9426567ba79 - - path: output/isoseq3/test.transcripts.hq.bam.pbi - md5sum: 4eecd253bb8cb0dbdc039ec80bb88ba0 - - path: output/isoseq3/test.transcripts.lq.bam - md5sum: 0bff3d6c3d1a2db1d4c0afced7d26d3b - - path: output/isoseq3/test.transcripts.lq.bam.pbi - md5sum: d1f96a5748c71d9eb1b69c620412c863 - - path: output/isoseq3/test.transcripts.singletons.bam - md5sum: 611fc52d0e1608a783bf3d7ac6f5edb6 - - path: output/isoseq3/test.transcripts.singletons.bam.pbi - md5sum: f63eed07e30bc66a72c6ebd24d0116e0 - - path: output/isoseq3/test.transcripts.transcriptset.xml - contains: ["PacBio.DataSet.TranscriptSet"] diff --git a/tests/modules/nf-core/isoseq3/refine/main.nf b/tests/modules/nf-core/isoseq3/refine/main.nf deleted file mode 100644 index 1ebafad4af2..00000000000 --- a/tests/modules/nf-core/isoseq3/refine/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ISOSEQ3_REFINE } from '../../../../../modules/nf-core/isoseq3/refine/main' - -workflow test_isoseq3_refine { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['lima'], checkIfExists: true), - ] - primers = file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) - - ISOSEQ3_REFINE ( input, primers ) -} diff --git a/tests/modules/nf-core/isoseq3/refine/test.yml b/tests/modules/nf-core/isoseq3/refine/test.yml deleted file mode 100644 index 190dfc2aae7..00000000000 --- a/tests/modules/nf-core/isoseq3/refine/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: isoseq3 refine test_isoseq3_refine - command: nextflow run ./tests/modules/nf-core/isoseq3/refine -entry test_isoseq3_refine -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/isoseq3/refine/nextflow.config - tags: - - isoseq3 - - isoseq3/refine - files: - - path: output/isoseq3/test.refine.bam - md5sum: 39028a7678496f5bb0a0285b24ff5145 - - path: output/isoseq3/test.refine.bam.pbi - md5sum: 28097cdf74c0d5d01c5f81a12dc22f5c - - path: output/isoseq3/test.refine.consensusreadset.xml - contains: ["pbds:ConsensusReadSet"] - - path: output/isoseq3/test.refine.filter_summary.report.json - contains: ["Created by pbcopper v2.1.0"] - - path: output/isoseq3/test.refine.report.csv - md5sum: d42a139e5d9b08396bdb087c01243ea9 - - path: output/isoseq3/versions.yml diff --git a/tests/modules/nf-core/lima/main.nf b/tests/modules/nf-core/lima/main.nf deleted file mode 100644 index 921b8dcba78..00000000000 --- a/tests/modules/nf-core/lima/main.nf +++ /dev/null @@ -1,60 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { LIMA } from '../../../../modules/nf-core/lima/main.nf' - -workflow test_lima_bam { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['ccs'], checkIfExists: true), - ] - primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] - - LIMA ( input, primers ) -} - -workflow test_lima_fa { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['ccs_fa'], checkIfExists: true), - ] - primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] - - LIMA ( input, primers ) -} - -workflow test_lima_fa_gz { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['ccs_fa_gz'], checkIfExists: true), - ] - primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] - - LIMA ( input, primers ) -} - -workflow test_lima_fq { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['ccs_fq'], checkIfExists: true), - ] - primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] - - LIMA ( input, primers ) -} - -workflow test_lima_fq_gz { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true), - ] - primers = [ file(params.test_data['homo_sapiens']['pacbio']['primers'], checkIfExists: true) ] - - LIMA ( input, primers ) -} diff --git a/tests/modules/nf-core/lima/nextflow.config b/tests/modules/nf-core/lima/nextflow.config deleted file mode 100644 index 8da2613f029..00000000000 --- a/tests/modules/nf-core/lima/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: LIMA { - ext.args = '--isoseq --peek-guess' - ext.prefix = { "${meta.id}.fl" } - } - -} diff --git a/tests/modules/nf-core/lima/test.yml b/tests/modules/nf-core/lima/test.yml deleted file mode 100644 index 48588cbd0f6..00000000000 --- a/tests/modules/nf-core/lima/test.yml +++ /dev/null @@ -1,114 +0,0 @@ -- name: lima test_lima_bam - command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config - tags: - - lima - files: - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam - md5sum: 00a79f1742c4883a218afda9192a3a14 - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi - md5sum: 6b09e46babe3e36a453639f7d76ab7c1 - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.consensusreadset.xml - contains: ["ConsensusReadSet"] - - path: output/lima/test.fl.consensusreadset.xml - contains: ["ConsensusReadSet"] - - path: output/lima/test.fl.json - contains: ["ConsensusReadSet"] - - path: output/lima/test.fl.lima.clips - md5sum: fa03bc75bd78b2648a139fd67c69208f - - path: output/lima/test.fl.lima.counts - md5sum: 842c6a23ca2de504ced4538ad5111da1 - - path: output/lima/test.fl.lima.guess - md5sum: d3675af3ca8a908ee9e3c231668392d3 - - path: output/lima/test.fl.lima.report - md5sum: dc073985322ae0a003ccc7e0fa4db5e6 - - path: output/lima/test.fl.lima.summary - md5sum: bcbcaaaca418bdeb91141c81715ca420 - - path: output/lima/versions.yml - -- name: lima test_lima_fa - command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fa -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config - tags: - - lima - files: - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam - md5sum: c5d3d376ca7ffc32ef5cbabcc9850804 - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi - md5sum: d1d6a2f961b9fb3d29837555706c59eb - - path: output/lima/test.fl.lima.clips - md5sum: 1012bc8874a14836f291bac48e8482a4 - - path: output/lima/test.fl.lima.counts - md5sum: a4ceaa408be334eaa711577e95f8730e - - path: output/lima/test.fl.lima.guess - md5sum: 651e5f2b438b8ceadb3e06a2177e1818 - - path: output/lima/test.fl.lima.report - md5sum: bd4a8bde17471563cf91aab4c787911d - - path: output/lima/test.fl.lima.summary - md5sum: 03be2311ba4afb878d8e547ab38c11eb - - path: output/lima/versions.yml - -- name: lima test_lima_fa_gz - command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fa_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config - tags: - - lima - files: - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam - md5sum: c5d3d376ca7ffc32ef5cbabcc9850804 - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi - md5sum: d1d6a2f961b9fb3d29837555706c59eb - - path: output/lima/test.fl.lima.clips - md5sum: 1012bc8874a14836f291bac48e8482a4 - - path: output/lima/test.fl.lima.counts - md5sum: a4ceaa408be334eaa711577e95f8730e - - path: output/lima/test.fl.lima.guess - md5sum: 651e5f2b438b8ceadb3e06a2177e1818 - - path: output/lima/test.fl.lima.report - md5sum: bd4a8bde17471563cf91aab4c787911d - - path: output/lima/test.fl.lima.summary - md5sum: 03be2311ba4afb878d8e547ab38c11eb - - path: output/lima/versions.yml - -- name: lima test_lima_fq - command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config - tags: - - lima - files: - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam - md5sum: c5d3d376ca7ffc32ef5cbabcc9850804 - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi - md5sum: d1d6a2f961b9fb3d29837555706c59eb - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq - md5sum: ef395f689c5566f501e300bb83d7a5f2 - - path: output/lima/test.fl.lima.clips - md5sum: 5c16ef8122f6f1798acc30eb8a30828c - - path: output/lima/test.fl.lima.counts - md5sum: 767b687e6eda7b24cd0e577f527eb2f0 - - path: output/lima/test.fl.lima.guess - md5sum: 31b988aab6bda84867e704b9edd8a763 - - path: output/lima/test.fl.lima.report - md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd - - path: output/lima/test.fl.lima.summary - md5sum: e91d3c386aaf4effa63f33ee2eb7da2a - - path: output/lima/versions.yml - -- name: lima test_lima_fq_gz - command: nextflow run ./tests/modules/nf-core/lima -entry test_lima_fq_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lima/nextflow.config - tags: - - lima - files: - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam - md5sum: c5d3d376ca7ffc32ef5cbabcc9850804 - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi - md5sum: d1d6a2f961b9fb3d29837555706c59eb - - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz - md5sum: 32c11db85f69a1b4454b6bbd794b6df2 - - path: output/lima/test.fl.lima.clips - md5sum: 5c16ef8122f6f1798acc30eb8a30828c - - path: output/lima/test.fl.lima.counts - md5sum: 767b687e6eda7b24cd0e577f527eb2f0 - - path: output/lima/test.fl.lima.guess - md5sum: 31b988aab6bda84867e704b9edd8a763 - - path: output/lima/test.fl.lima.report - md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd - - path: output/lima/test.fl.lima.summary - md5sum: e91d3c386aaf4effa63f33ee2eb7da2a - - path: output/lima/versions.yml diff --git a/tests/modules/nf-core/pbccs/main.nf b/tests/modules/nf-core/pbccs/main.nf deleted file mode 100644 index 17c8f8e0992..00000000000 --- a/tests/modules/nf-core/pbccs/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PBCCS } from '../../../../modules/nf-core/pbccs/main.nf' - -workflow test_pbccs { - - input = [ - [ id:'alz' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['alz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true) - ] - - chunk_num = 2 - chunk_on = 3 - - PBCCS ( input, chunk_num, chunk_on ) -} diff --git a/tests/modules/nf-core/pbccs/test.yml b/tests/modules/nf-core/pbccs/test.yml deleted file mode 100644 index f06af1fcd5d..00000000000 --- a/tests/modules/nf-core/pbccs/test.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: pbccs test_pbccs - command: nextflow run ./tests/modules/nf-core/pbccs -entry test_pbccs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pbccs/nextflow.config - tags: - - pbccs - files: - - path: output/pbccs/alz.chunk2.bam - md5sum: 306ba0287e3c7f4cd8f5af577af7ac62 - - path: output/pbccs/alz.chunk2.bam.pbi - md5sum: 36c3d2843aae90739ee8ca82d27abd55 - - path: output/pbccs/alz.chunk2.metrics.json.gz - contains: ["zmws"] - - path: output/pbccs/alz.chunk2.report.json - contains: ["Created by pbcopper"] - - path: output/pbccs/alz.chunk2.report.txt - md5sum: 67583febb144333e3f854c7bf4a17a50