BUG metaAssembly job Failed to import make_interleaved_WDL

[mbthornton-lbl]

Failed metaAssembly metadata:

{
  "workflowProcessingEvents": [
    {
      "cromwellId": "cromid-b6a74b9",
      "description": "PickedUp",
      "timestamp": "2025-03-05T01:21:36.028Z",
      "cromwellVersion": "77"
    },
    {
      "cromwellId": "cromid-b6a74b9",
      "description": "Finished",
      "timestamp": "2025-03-05T01:21:37.193Z",
      "cromwellVersion": "77"
    }
  ],
  "actualWorkflowLanguageVersion": "1.0",
  "submittedFiles": {
    "workflow": "version 1.0\nimport \"shortReads_assembly.wdl\" as srma\nimport \"make_interleaved_WDL/make_interleaved_reads.wdl\" as int\nimport \"https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/raw/bc7c4371ea0fa83355bada341ec353b9feb3eff2/metagenome_improved/metaflye.wdl\" as lrma\n\nworkflow jgi_metaAssembly {\n    input {  \n        Boolean shortRead\n        String proj\n        String prefix=sub(proj, \":\", \"_\")\n        # shortReads parameters\n        String? memory\n        String? threads\n        # longReads parameters\n        Array[String] input_files\n        String flye_container = \"staphb/flye:2.9.2\"\n        String flye_parameters = \"--meta -o flye -t 32 --pacbio-hifi\"\n        String smrtlink_container = \"bryce911/smrtlink:12.0.0.177059\"\n        String racon_container = \"staphb/racon:1.4.20\"\n        String minimap2_container = \"staphb/minimap2:2.25\"\n        String minimap2_parameters = \"-a -x map-hifi -t 32\"\n        String samtools_container = \"staphb/samtools:1.18\"\n        String bbtools_container = \"microbiomedata/bbtools:39.03\"\n        String spades_container=\"staphb/spades:4.0.0\"\n    }\n\n\n    if (shortRead) {\n    \tif (length(input_files) > 1) {\n        \tcall int.make_interleaved_reads {\n                input:\n                    input_files = input_files,\n                    container = \"microbiomedata/bbtools:38.96\"\n       \t\t}\n    \t}\n        call srma.jgi_metaASM {\n            input:\n                memory = memory,\n                threads = threads,\n                input_file = if length(input_files) > 1 then make_interleaved_reads.interleaved_fastq else input_files[0],\n                proj = proj,\n                bbtools_container = \"microbiomedata/bbtools:38.96\",\n                spades_container = spades_container\n        }\n        \n    }\n    if (!shortRead) {\n        call lrma.metaflye {\n            input:\n                proj = proj,\n                input_fastq = input_files,\n                flye_container = flye_container,\n                flye_parameters = flye_parameters,\n                smrtlink_container = smrtlink_container, \n                racon_container = racon_container,\n                minimap2_container = minimap2_container,\n                minimap2_parameters = minimap2_parameters, \n                samtools_container = samtools_container,\n                bbtools_container = bbtools_container\n        }\n        call finish_lrasm {\n            input: \n                proj = proj,\n                prefix = prefix,\n                container = bbtools_container,\n                contigs = metaflye.final_contigs,\n                bam = metaflye.final_bam, \n                scaffolds = metaflye.final_scaffolds,\n                agp = metaflye.final_agp,\n                legend = metaflye.final_legend,\n                basecov = metaflye.final_basecov,\n                sam = metaflye.final_sam,    \n                output_file = metaflye.final_output_file,\n                stats = metaflye.final_stats,\n                summary_stats = metaflye.final_summary_stats,\n                pileup_out = metaflye.final_pileup_out\n        }\n    }\n    output {\n        # long reads output\n        File? lr_contigs = finish_lrasm.final_contigs\n        File? lr_bam = finish_lrasm.final_bam \n        File? lr_scaffolds = finish_lrasm.final_scaffolds\n        File? lr_agp = finish_lrasm.final_agp\n        File? lr_legend = finish_lrasm.final_legend\n        File? lr_basecov = finish_lrasm.final_basecov\n        File? lr_sam = finish_lrasm.final_sam    \n        File? lr_output_file = finish_lrasm.final_output_file\n        File? lr_stats = finish_lrasm.final_stats\n        File? lr_summary_stats = finish_lrasm.final_summary_stats\n        File? lr_pileup_out = finish_lrasm.final_pileup_out\n        File? lr_asminfo = metaflye.asminfo\n\n        # short reads output\n        File? sr_contig=jgi_metaASM.contig\n        File? sr_scaffold=jgi_metaASM.scaffold\n        File? sr_agp=jgi_metaASM.agp\n        File? sr_bam=jgi_metaASM.bam\n        File? sr_samgz=jgi_metaASM.samgz\n        File? sr_covstats=jgi_metaASM.covstats\n        File? sr_asminfo=jgi_metaASM.asminfo\n        File? sr_bbcms_fq = jgi_metaASM.bbcms_fastq\n\n        #Both\n        File? stats = if (shortRead) then jgi_metaASM.asmstats else finish_lrasm.asm_stats\n    }\n}\n\n\ntask finish_lrasm {\n    input {\n        File contigs\n        File bam\n        File scaffolds\n        File agp\n        File legend\n        File basecov\n        File sam\n        File output_file\n        File stats\n        File summary_stats\n        File pileup_out\n        String container\n        String proj\n        String prefix \n        String orig_prefix=\"scaffold\"\n        String sed=\"s/~{orig_prefix}_/~{proj}_/g\"\n        # String start\n    }\n    command<<<\n\n        set -oeu pipefail\n        end=`date --iso-8601=seconds`\n        ln -s ~{output_file} ~{prefix}_read_count_report.txt\n        ln -s ~{stats} ~{prefix}_contigs.sam.stats\n        ln -s ~{summary_stats} ~{prefix}_summary.stats\n\n        ##RE-ID\n        cat ~{contigs} | sed ~{sed} > ~{prefix}_contigs.fna\n        cat ~{scaffolds} | sed ~{sed} > ~{prefix}_scaffolds.fna\n        cat ~{agp} | sed ~{sed} > ~{prefix}_assembly.agp\n        cat ~{legend} | sed ~{sed} > ~{prefix}_assembly.legend\n        cat ~{basecov} | sed ~{sed} > ~{prefix}_contigs.sorted.bam.pileup.basecov\n        cat ~{pileup_out} | sed ~{sed} > ~{prefix}_contigs.sorted.bam.pileup.out\n\n        ## Bam file     \n        samtools view -h ~{bam} | sed ~{sed} | \\\n            samtools view -hb -o ~{prefix}_pairedMapped_sorted.bam\n        ## Sam.gz file\n        samtools view -h ~{sam} | sed ~{sed} | \\\n            gzip -c - > ~{prefix}_pairedMapped.sam.gz\n        \n        # stats file\n        bbstats.sh format=8 in=~{scaffolds} out=stats.json\n        sed -i 's/l_gt50k/l_gt50K/g' stats.json\n        cat stats.json |jq 'del(.filename)' > stats.json\n\n    >>>\n    output {\n        File final_contigs = \"~{prefix}_contigs.fna\"\n        File final_bam = \"~{prefix}_pairedMapped_sorted.bam\"\n        File final_scaffolds = \"~{prefix}_scaffolds.fna\"\n        File final_agp = \"~{prefix}_assembly.agp\"\n        File final_legend = \"~{prefix}_assembly.legend\"\n        File final_basecov = \"~{prefix}_contigs.sorted.bam.pileup.basecov\"\n        File final_sam = \"~{prefix}_pairedMapped.sam.gz\"  \n        File final_output_file = \"~{prefix}_read_count_report.txt\"\n        File final_stats = \"~{prefix}_contigs.sam.stats\"\n        File final_summary_stats = \"~{prefix}_summary.stats\"\n        File final_pileup_out = \"~{prefix}_contigs.sorted.bam.pileup.out\"\n        File asm_stats = \"stats.json\"\n    }\n\n    runtime {\n        docker: container\n        memory: \"1 GiB\"\n        cpu:  1\n    }\n}\n",
    "root": "",
    "options": "{\n\n}",
    "inputs": "{\"jgi_metaAssembly.input_files\":\"https://data.microbiomedata.org/data/nmdc:omprc-11-df59n582/nmdc:wfrqc-12-c7w3sr53.1/nmdc_wfrqc-12-c7w3sr53.1_filtered.fastq.gz\",\"jgi_metaAssembly.proj\":\"nmdc:wfmgas-12-hh1e8n50.1\",\"jgi_metaAssembly.shortRead\":false}",
    "workflowUrl": "",
    "labels": "{\"release\": \"v1.0.7\", \"wdl\": \"jgi_assembly.wdl\", \"git_repo\": \"https://github.com/microbiomedata/metaAssembly\", \"submitter\": \"nmdcda\", \"pipeline_version\": \"v1.0.7\", \"pipeline\": \"jgi_assembly.wdl\", \"activity_id\": \"nmdc:wfmgas-12-hh1e8n50.1\", \"opid\": \"nmdc:sys05yc8cs41\"}"
  },
  "calls": {},
  "outputs": {},
  "actualWorkflowLanguage": "WDL",
  "id": "797cbb3a-5a5f-40e6-ad03-4ec94d68d9f6",
  "inputs": {},
  "labels": {
    "wdl": "jgi_assembly.wdl",
    "git_repo": "https://github.com/microbiomedata/metaAssembly",
    "pipeline_version": "v1.0.7",
    "cromwell-workflow-id": "cromwell-797cbb3a-5a5f-40e6-ad03-4ec94d68d9f6",
    "pipeline": "jgi_assembly.wdl",
    "opid": "nmdc:sys05yc8cs41",
    "activity_id": "nmdc:wfmgas-12-hh1e8n50.1",
    "submitter": "nmdcda",
    "release": "v1.0.7"
  },
  "submission": "2025-03-05T01:21:25.808Z",
  "status": "Failed",
  "failures": [
    {
      "causedBy": [
        {
          "causedBy": [],
          "message": "Failed to import 'make_interleaved_WDL/make_interleaved_reads.wdl' (reason 1 of 2): Failed to resolve 'make_interleaved_WDL/make_interleaved_reads.wdl' using resolver: 'relative to directory [...]/imports_workflow_797cbb3a-5a5f-40e6-ad03-4ec94d68d9f6_157174995232085516701874229145056499296 (without escaping [...]/imports_workflow_797cbb3a-5a5f-40e6-ad03-4ec94d68d9f6_157174995232085516701874229145056499296)' (reason 1 of 1): File not found: make_interleaved_WDL/make_interleaved_reads.wdl"
        },
        {
          "causedBy": [],
          "message": "Failed to import 'make_interleaved_WDL/make_interleaved_reads.wdl' (reason 2 of 2): Failed to resolve 'make_interleaved_WDL/make_interleaved_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path"
        }
      ],
      "message": "Workflow input processing failed"
    }
  ],
  "end": "2025-03-05T01:21:37.193Z",
  "start": "2025-03-05T01:21:36.028Z"
}