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feat(export): initial emgb export functionality
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,47 @@ | ||
| tempdir: "tmp" | ||
| summary: false | ||
| s3SignIn: false | ||
| input: "output" | ||
| output: "output" | ||
| logDir: log | ||
| runid: 1 | ||
| databases: "/mnt/databases" | ||
| logLevel: 1 | ||
| scratch: "/vol/scratch" | ||
| publishDirMode: "symlink" | ||
| steps: | ||
| export: | ||
| emgb: | ||
| titles: | ||
| database: | ||
| download: | ||
| source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/uniref90.titles.tsv.gz" | ||
| md5sum: aaf1dd9021243def8e6c4e438b4b3669 | ||
| kegg: | ||
| database: | ||
| download: | ||
| source: s3://databases_internal/annotatedgenes2json_db_kegg-mirror-2022-12.tar.zst | ||
| md5sum: 262dab8ca564fbc1f27500c22b5bc47b | ||
| s5cmd: | ||
| params: '--retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080' | ||
| resources: | ||
| highmemLarge: | ||
| cpus: 28 | ||
| memory: 230 | ||
| highmemMedium: | ||
| cpus: 14 | ||
| memory: 113 | ||
| large: | ||
| cpus: 28 | ||
| memory: 58 | ||
| medium: | ||
| cpus: 14 | ||
| memory: 29 | ||
| small: | ||
| cpus: 7 | ||
| memory: 14 | ||
| tiny: | ||
| cpus: 1 | ||
| memory: 1 | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,165 @@ | ||
| include { pDumpLogs } from '../utils/processes' | ||
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| def getOutput(SAMPLE, RUNID, TOOL, filename){ | ||
| return SAMPLE + '/' + RUNID + '/' + params.modules.export.name + '/' + | ||
| params.modules.export.version.major + "." + | ||
| params.modules.export.version.minor + "." + | ||
| params.modules.export.version.patch + | ||
| '/' + TOOL + '/' + filename | ||
| } | ||
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| process pEMGBAnnotatedContigs { | ||
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| container "${params.emgbAnnotatedContigs_image}" | ||
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| tag "Sample: $sample" | ||
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| publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "emgb", filename) } | ||
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| when params.steps.containsKey("export") && params.steps.export.containsKey("emgb") | ||
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| containerOptions " --entrypoint='' " | ||
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| label 'tiny' | ||
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| input: | ||
| tuple val(sample), path(contigs), path(mapping), path("bins/*") | ||
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| output: | ||
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| tuple val("${sample}"), path("${sample}.contigs.json.gz"), emit: json | ||
| tuple env(FILE_ID), val("${output}"), val(params.LOG_LEVELS.INFO), file(".command.sh"), \ | ||
| file(".command.out"), file(".command.err"), file(".command.log"), emit: logs | ||
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| shell: | ||
| template 'emgbAnnotatedContigs.sh' | ||
| } | ||
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| process pEMGBAnnotatedBins { | ||
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| container "${params.emgbAnnotatedBins_image}" | ||
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| tag "Sample: $sample" | ||
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| publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "emgb", filename) } | ||
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| when params.steps.containsKey("export") && params.steps.export.containsKey("emgb") | ||
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| containerOptions " --entrypoint='' " | ||
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| label 'tiny' | ||
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| input: | ||
| tuple val(sample), path(checkm), path(gtdbtk), path("bins/*") | ||
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| output: | ||
| tuple val("${sample}"), path("${sample}.bins.json.gz"), emit: json | ||
| tuple env(FILE_ID), val("${output}"), val(params.LOG_LEVELS.INFO), file(".command.sh"), \ | ||
| file(".command.out"), file(".command.err"), file(".command.log"), emit: logs | ||
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| shell: | ||
| template 'emgbAnnotatedBins.sh' | ||
| } | ||
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| process pEMGBAnnotatedGenes { | ||
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| container "${params.emgbAnnotatedGenes_image}" | ||
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| tag "Sample: $sample" | ||
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| publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "emgb", filename) } | ||
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| secret { "${S3_EMGB_TITLES_ACCESS}"!="" ? ["S3_EMGB_TITLES_ACCESS", "S3_EMGB_TITLES_SECRET"] : [] } | ||
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| secret { "${S3_EMGB_KEGG_ACCESS}"!="" ? ["S3_EMGB_KEGG_ACCESS", "S3_EMGB_KEGG_SECRET"] : [] } | ||
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| containerOptions Utils.getDockerMount(params.steps?.export?.emgb?.titles?.database, params) + Utils.getDockerMount(params.steps?.export?.emgb?.kegg?.database, params) + Utils.getDockerNetwork() + " --entrypoint='' " | ||
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| when params.steps.containsKey("export") && params.steps.export.containsKey("emgb") | ||
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| memory { Utils.getMemoryResources(params.resources.medium, "${sample}", task.attempt, params.resources) } | ||
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| cpus { Utils.getCPUsResources(params.resources.medium, "${sample}", task.attempt, params.resources) } | ||
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| beforeScript Utils.getCreateDatabaseDirCommand("${params.polished.databases}") | ||
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| input: | ||
| tuple val(sample), path("gff/*"), path("ffn/*"), path("faa/*"), path("taxonomy/*"), path("blastResult/*"), path("blastKeggResult/*"), path("bins/*") | ||
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| output: | ||
| tuple val("${sample}"), path("${sample}.genes.json.gz"), emit: json | ||
| tuple env(FILE_ID), val("${output}"), val(params.LOG_LEVELS.INFO), file(".command.sh"), \ | ||
| file(".command.out"), file(".command.err"), file(".command.log"), emit: logs | ||
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| shell: | ||
| TITLES_S5CMD_PARAMS=params?.steps?.export?.emgb?.titles?.database?.download?.s5cmd?.params ?: "" | ||
| TITLES_DOWNLOAD_LINK=params?.steps?.export?.emgb?.titles?.database?.download?.source ?: "" | ||
| TITLES_MD5SUM=params.steps?.export?.emgb?.titles?.database?.download?.md5sum ?: "" | ||
| TITLES_EXTRACTED_DB=params.steps?.export?.emgb?.titles?.database?.extractedDBPath ?: "" | ||
| KEGG_S5CMD_PARAMS=params?.steps?.export?.emgb?.kegg?.database?.download?.s5cmd?.params ?: "" | ||
| KEGG_DOWNLOAD_LINK=params?.steps?.export?.emgb?.kegg?.database?.download?.source ?: "" | ||
| KEGG_MD5SUM=params.steps?.export?.emgb?.kegg?.database?.download?.md5sum ?: "" | ||
| KEGG_EXTRACTED_DB=params.steps?.export?.emgb?.kegg?.database?.extractedDBPath ?: "" | ||
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| TITLES_S3_EMGB_ACCESS=params?.steps?.export?.emgb?.titles?.database?.download?.s5cmd && TITLES_S5CMD_PARAMS.indexOf("--no-sign-request") == -1 ? "\$S3_EMGB_TITLES_ACCESS" : "" | ||
| TITLES_S3_EMGB_SECRET=params?.steps?.export?.emgb?.titles?.database?.download?.s5cmd && TITLES_S5CMD_PARAMS.indexOf("--no-sign-request") == -1 ? "\$S3_EMGB_TITLES_SECRET" : "" | ||
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| KEGG_S3_EMGB_ACCESS=params?.steps?.export?.emgb?.kegg?.database?.download?.s5cmd && KEGG_S5CMD_PARAMS.indexOf("--no-sign-request") == -1 ? "\$S3_EMGB_KEGG_ACCESS" : "" | ||
| KEGG_S3_EMGB_SECRET=params?.steps?.export?.emgb?.kegg?.database?.download?.s5cmd && KEGG_S5CMD_PARAMS.indexOf("--no-sign-request") == -1 ? "\$S3_EMGB_KEGG_SECRET" : "" | ||
| template 'emgbAnnotatedGenes.sh' | ||
| } | ||
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| // CONTIGS: [test1, /vol/spool/metagenomics-tk/work_wFullPipeline/cd/7c943c0808e6d36c72a64834e7a88e/test1_contigs.fa.gz] | ||
| // [test2, /vol/spool/metagenomics-tk/work_wFullPipeline/00/71fd0e590f4f03fda4cb87903a3b38/test2_contigs.fa.gz] | ||
| // mapping: [test2, /vol/spool/metagenomics-tk/work_wFullPipeline/7c/43a3513d49143a76a29c4404417997/test2.bam] | ||
| // bins: [test1, [/vol/spool/metagenomics-tk/work_wFullPipeline/95/085ffbe17a6f2ebfb60709d3f33cf3/test1_bin.1.fa, /vol/spool/metagenomics-tk/work_wFullPipeline/95/085ffbe17a6f2ebfb60709d3f33cf3/test1_bin.2.fa]] | ||
| // gtdbtk: [test2, [/vol/spool/metagenomics-tk/work_wFullPipeline/d2/5b5937c7a950d87cd796e2bf80cfcd/chunk_00_test2_gtdbtk.bac120.summary.tsv]] | ||
| // checkm: [test2, /vol/spool/metagenomics-tk/work_wFullPipeline/ff/1292ed3399aada6fa1dffc18cfbc12/test2_checkm2_EfY2cPIh.tsv] | ||
| // gff,ffn,faa: [test2, test2_bin.2.fa, /vol/spool/metagenomics-tk/work_wFullPipeline/78/1224783c7ae2d9e0a8d4264893e47a/test2_bin.2.gff.gz] | ||
| // mmseqsTaxonomy: [ncbi_nr, test1, /vol/spool/metagenomics-tk/work_wFullPipeline/93/56bf5c34d7524930d73a6ef45ae23d/test1_binned.ncbi_nr.taxonomy.tsv] | ||
| //mmseqsBlast: | ||
| // [bacmet20_predicted, test2, binned, 1, 2922, 1, /vol/spool/metagenomics-tk/work_wFullPipeline/3c/e5221be7fd305dc056356201de7d61/test2_binned.1.2922.bacmet20_predicted.blast.tsv] | ||
| // [uniref90, test1, binned, 1, 2923, 1, /vol/spool/metagenomics-tk/work_wFullPipeline/a0/8e7a2a7b928731dbcfd62cbf546d4f/test1_binned.1.2923.uniref90.blast.tsv] | ||
| // [bacmet20_predicted, test1, binned, 1, 2923, 1, /vol/spool/metagenomics-tk/work_wFullPipeline/2f/dffc66ee85b2a1baf296323fcc894c/test1_binned.1.2923.bacmet20_predicted.blast.tsv] | ||
| // [kegg, test2, binned, 1, 2922, 1, /vol/spool/metagenomics-tk/work_wFullPipeline/5a/74adca85c1b4005aa490440f8b05ba/test2_binned.1.2922.kegg.blast.tsv] | ||
| // [uniref90, test2, binned, 1, 2922, 1, /vol/spool/metagenomics-tk/work_wFullPipeline/57/5f4e7f5ae75937613d7c813be6c8fd/test2_binned.1.2922.uniref90.blast.tsv] | ||
| // [kegg, test1, binned, 1, 2923, 1, /vol/spool/metagenomics-tk/work_wFullPipeline/6b/41a5ce820f9fb5e897b6a9109e5678/test1_binned.1.2923.kegg.blast.tsv] | ||
| workflow wEMGBList { | ||
| take: | ||
| contigs | ||
| mapping | ||
| bins | ||
| gtdbtk | ||
| checkm | ||
| gff | ||
| ffn | ||
| faa | ||
| mmseqsTaxonomy | ||
| mmseqsBlast | ||
| main: | ||
| SAMPLE_IDX = 0 | ||
| contigs | combine(mapping, by: SAMPLE_IDX) | combine(bins, by: SAMPLE_IDX) | pEMGBAnnotatedContigs | ||
| checkm | combine(gtdbtk, by: SAMPLE_IDX) | combine(bins, by: SAMPLE_IDX) | pEMGBAnnotatedBins | ||
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| mmseqsBlast | filter { db, sample, type, start, end, chunkNumber, blastResult -> db == "uniref90" } \ | ||
| | map { db, sample, type, start, end, chunkNumber, blastResult -> [sample, blastResult] } \ | ||
| | groupTuple(by: SAMPLE_IDX) | set { selectedDBBlastResults } | ||
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| mmseqsBlast | filter { db, sample, type, start, end, chunkNumber, blastResult -> db == "kegg" } \ | ||
| | map { db, sample, type, start, end, chunkNumber, blastResult -> [sample, blastResult] } \ | ||
| | groupTuple(by: SAMPLE_IDX) | set { selectedKeggBlastResults } | ||
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| gff | map { sample, bin, gff -> [sample, gff] } | groupTuple(by: SAMPLE_IDX) \ | ||
| | combine(ffn | map { sample, bin, ffn -> [sample, ffn] } | groupTuple(by: SAMPLE_IDX), by: SAMPLE_IDX) \ | ||
| | combine(faa | map { sample, bin, faa -> [sample, faa] } | groupTuple(by: SAMPLE_IDX), by: SAMPLE_IDX) \ | ||
| | combine(mmseqsTaxonomy | map { db, sample, blastResult -> [sample, blastResult] } | groupTuple(by: SAMPLE_IDX), by: SAMPLE_IDX) \ | ||
| | combine(selectedDBBlastResults, by: SAMPLE_IDX) \ | ||
| | combine(selectedKeggBlastResults, by: SAMPLE_IDX) \ | ||
| | combine(bins, by: SAMPLE_IDX) | pEMGBAnnotatedGenes | ||
| } |
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