Cannot make job: :1:1: Expression evaluation error:

---

Expected Behavior

This was a working WF at version 1.0.20170622090721, should execute to completion. I cleaned out ~/.local then pip install --user cwltool

Actual Behavior

Fails on first step, see below.

Workflow Code

#!/usr/bin/env cwl-runner

class: Workflow
cwlVersion: v1.0

requirements:
- $import: tools/trimmomatic-types.yml
- $import: tools/envvar-global.yml
- class: InlineJavascriptRequirement
  expressionLib:
  - var rename_trim_file = function() {
      if ( self == null ) {
        return null;
      } else {
        var xx = self.basename.split('.');
        var id = xx.indexOf('fastq');
        xx.splice(id, 1);
        return xx.join('.');
      }
    };
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement

inputs:
  read1: File
  read2: File

outputs:
  # trim with trimmomatic and rename
  trim-logs:
    type: File
    outputSource: trim/output_log
  rename_reads1_trimmed_file:
    type: File
    outputSource: rename_reads1_trimmed/renamed
  rename_reads2_trimmed_paired_file:
    type: File
    outputSource: trim/reads2_trimmed_unpaired
  reads1_trimmed_unpaired_file:
    type: File
    outputSource: trim/reads1_trimmed_unpaired
  reads2_trimmed_unpaired_file:
    type: File
    outputSource: trim/reads2_trimmed_unpaired
  # align to mouse with bowtie2
  mouse-aligned:
    type: File
    outputSource: align-to-mouse/aligned-file
  # align to human with bowtie2
  human-aligned:
    type: File
    outputSource: align-to-human/aligned-file
  # convert
  human-sorted:
    type: File
    streamable: true
    outputSource: convert-human/output
  # sort and compress
  human-compress:
    type: File
    outputSource: sort-human/sorted
  # Index human bam
  human-index:
    type: File
    outputSource: index-human/index
  # compare genomes with xenomapper
  primary_specific:
    type: File?
    outputSource: xenomapping/primary_specific
  secondary_specific:
    type: File?
    outputSource: xenomapping/secondary_specific
  primary_multi:
    type: File?
    outputSource: xenomapping/primary_multi
  secondary_multi:
    type: File?
    outputSource: xenomapping/secondary_multi
  unassigned:
    type: File?
    outputSource: xenomapping/unassigned
  unresolved:
    type: File?
    outputSource: xenomapping/unresolved
  # pileip
  human-mpileup:
    type: File
    outputSource: mpileup-human/output
  # varscan output
  varscan:
    type: File
    outputSource: varscan-human/output
  # platypus output
  platypus-vcf:
    type: File
    outputSource: platypus/output
  # gridss
  gridss:
    type: File
    outputSource: gridss-human/output

steps:

  #
  # trim with trimmomatic
  #
  trim:
    run: tools/trimmomatic.cwl

    in:
      reads1:
        source: read1
        valueFrom: >
          ${
              self.format = "http://edamontology.org/format_1930";
              return self;
          }
      reads2:
        source: read2
        valueFrom: >
          ${
              self.format = "http://edamontology.org/format_1930";
              return self;
          }
      end_mode:
        default: PE
      nthreads:
        valueFrom: ${ return 8; }
      illuminaClip:
        default:
          adapters:
            class: File
            location: "/stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa"
          seedMismatches: 1
          palindromeClipThreshold: 20
          simpleClipThreshold: 20
          minAdapterLength: 4
          keepBothReads: "true"

    out: [output_log, reads1_trimmed, reads1_trimmed_unpaired, reads2_trimmed_paired, reads2_trimmed_unpaired]

  #
  # rename trimmed files by removing redundant '.fastq' from the filename
  #
  rename_reads1_trimmed:
    run: tools/rename-file.cwl

    in:
      infile: trim/reads1_trimmed
      outfile:
        source: trim/reads1_trimmed
        valueFrom: >
          ${
              return rename_trim_file();
          }

    out: [renamed]

  rename_reads2_trimmed_paired:
    run: tools/rename-file.cwl

    in:
      infile: trim/reads2_trimmed_paired
      outfile:
        source: trim/reads2_trimmed_paired
        valueFrom: >
          ${
              return rename_trim_file();
          }

    out: [renamed]

  #
  # align to mouse reference with bowtie2
  #
  align-to-mouse:
    run: tools/bowtie2.cwl

    in:
      samout:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
              return self.nameroot + '.mouse.sam'
          }
      threads:
        valueFrom: ${ return 8; }
      one:
        source: trim/reads1_trimmed
        valueFrom: >
          ${
            return [self];
          }
      two:
        source: rename_reads2_trimmed_paired/renamed
        valueFrom: >
          ${
            if ( self == null ) {
              return null;
              } else {
              return [self];
            }
          }
      unpaired:
        source: trim/reads1_trimmed_unpaired
        valueFrom: >
          ${
            if ( self == null ) {
              return null;
              } else {
              return [self];
            }
          }
      bt2-idx:
        default: /stornext/HPCScratch/PapenfussLab/reference_genomes/bowtie2/GRCm38
      local:
        default: true
      reorder:
        default: true

    out: [aligned-file]

  #
  # align to human reference with bowtie2
  #
  align-to-human:
    run: tools/bowtie2.cwl

    in:
      samout:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
              return self.nameroot + '.human.sam'
          }
      threads:
        valueFrom: ${ return 8; }
      one:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return [self];
          }
      two:
        source: rename_reads2_trimmed_paired/renamed
        valueFrom: >
          ${
            if ( self == null ) {
              return null;
              } else {
              return [self];
            }
          }
      unpaired:
        source: trim/reads1_trimmed_unpaired
        valueFrom: >
          ${
            if ( self == null ) {
              return null;
              } else {
              return [self];
            }
          }
      bt2-idx:
        default: /wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/reference_genomes/human_new/no_alt/hg38_no_alt.fa
      local:
        default: true
      reorder:
        default: true

    out: [aligned-file]

  #
  # convert human
  #
  convert-human:
    run: tools/samtools-view.cwl

    in:
      input:
        align-to-human/aligned-file
      output_name:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
              return self.nameroot + '.human.bam'
          }
      threads:
        valueFrom: ${ return 8; }

    out: [output]

  #
  # sort and compress human
  #
  sort-human:
    run: tools/samtools-sort.cwl

    in:
      input:
        source: convert-human/output
      output_name:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
              return self.nameroot + '.sorted.human.bam'
          }
      threads:
        valueFrom: ${ return 8; }

    out: [sorted]

  #
  # index human bam
  #
  index-human:
    run: tools/samtools-index.cwl

    in:
      input:
        source: sort-human/sorted

    out: [index]

  #
  # human pileup file
  #
  mpileup-human:
    run: tools/samtools-mpileup.cwl

    in:
      bamFiles:
        source: sort-human/sorted
        valueFrom: >
          ${
              if ( self == null ) {
                return null;
              } else {
                return [self];
              }
            }

      output_fn:
        source: sort-human/sorted
        valueFrom: >
          ${
            return self.nameroot + '.pileup'
          }

    out: [output]

  #
  # varscan human
  #
  varscan-human:
    run: tools/varscan-mpileup2snp.cwl

    in:
      input:
        source: mpileup-human/output

      output-vcf:
        valueFrom: >
          ${
            return true;
          }

    out: [output]

  #
  # GRIDSS that human
  #
  gridss-human:
    run: tools/gridss-callvariants.cwl

    in:
      INPUT:
        source: sort-human/sorted
        valueFrom: >
          ${
              if ( self == null ) {
                return null;
              } else {
                return [self];
              }
            }

      REFERENCE_SEQUENCE:
        default: /wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/reference_genomes/human_new/no_alt/hg38_no_alt.fa

      OUTPUT:
        source: sort-human/sorted
        valueFrom: >
          ${
              return self.nameroot + '.gridss.vcf'
          }

      ASSEMBLY:
        source: sort-human/sorted
        valueFrom: >
          ${
              return self.nameroot + '.gridss.bam'
          }

    out: [output]

  #
  # xenomapper
  #
  xenomapping:
    run: tools/xenomapper.cwl

    in:
      primary_sam:
        source: align-to-human/aligned-file
      secondary_sam:
        source: align-to-mouse/aligned-file
      primary_specific_fn:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return self.nameroot + '.human_specific.sam'
          }
      secondary_specific_fn:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return self.nameroot + '.mouse_specific.sam'
          }
      primary_multi_fn:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return self.nameroot + '.human_multi.sam'
          }
      secondary_multi_fn:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return self.nameroot + '.mouse_multi.sam'
          }
      unassigned_fn:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return self.nameroot + '.unassigned.sam'
          }
      unresolved_fn:
        source: rename_reads1_trimmed/renamed
        valueFrom: >
          ${
            return self.nameroot + '.unresolved.sam'
          }

    out: [primary_specific, secondary_specific, primary_multi, secondary_multi, unassigned, unresolved]

  #
  # Gather human bam and index into one dependency
  #
  gather:
    run:
      class: ExpressionTool

      inputs:
        bamFile:
          type: File
        bamIndex:
          type: File

      outputs:
        combined:
          type: File

      expression: >
        ${
          var ret = inputs.bamFile;
          ret["secondaryFiles"] = [
            inputs.bamIndex
          ];
          return {"combined" : ret};
        }

    in:
      bamFile:
        source: sort-human/sorted
      bamIndex:
        source: index-human/index

    out: [combined]

  #
  # Call with platypus
  #
  platypus:
    run: tools/platypus.cwl

    in:
      bamFiles:
        source: gather/combined
        valueFrom: >
          ${
            if ( self == null ) {
              return null;
              } else {
              return [self];
            }
          }
      refFile:
        default: /wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/reference_genomes/human_new/no_alt/hg38_no_alt.fa
      outputFileName:
        source: sort-human/sorted
        valueFrom: >
          ${
              return self.nameroot + '.platypus.vcf'
          }
      verbosity:
        valueFrom: >
          ${
            return 0;
          }

    out: [output]

Full Traceback

$ cwltool --debug ../src/pdx-pl.cwl --read1 data/S1_R1.fastq.gz --read2 data/S1_R2.fastq.gz 
/home/thomas.e/.local/bin/cwltool 1.0.20170803160545
Resolved '../src/pdx-pl.cwl' to 'file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl'
No handlers could be found for logger "rdflib.term"
Workflow checker warning:
../src/pdx-pl.cwl:140:39: Source 'reads1_trimmed_unpaired' of type ["null", "File"] is partially incompatible
../src/pdx-pl.cwl:40:5:   with sink 'reads1_trimmed_unpaired_file' of type "File"
../src/pdx-pl.cwl:140:87: Source 'reads2_trimmed_unpaired' of type ["null", "File"] is partially incompatible
../src/pdx-pl.cwl:43:5:   with sink 'reads2_trimmed_unpaired_file' of type "File"
../src/pdx-pl.cwl:140:87: Source 'reads2_trimmed_unpaired' of type ["null", "File"] is partially incompatible
../src/pdx-pl.cwl:37:5:   with sink 'rename_reads2_trimmed_paired_file' of type "File"
Parsed job order from command line: {
    "read1": {
        "class": "File", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz"
    }, 
    "read2": {
        "class": "File", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz"
    }, 
    "id": "../src/pdx-pl.cwl"
}
[workflow pdx-pl.cwl] initialized from file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl
[workflow pdx-pl.cwl] start
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#rename_reads2_trimmed_paired not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#platypus not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#convert-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#align-to-mouse not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#gather not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#gridss-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#varscan-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#align-to-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#index-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#sort-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#xenomapping not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#mpileup-human not ready
[workflow pdx-pl.cwl] job step file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#rename_reads1_trimmed not ready
[workflow pdx-pl.cwl] starting step trim
[job step trim] job input {
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/illuminaClip": {
        "adapters": {
            "class": "File", 
            "location": "file:///stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa"
        }, 
        "seedMismatches": 1, 
        "palindromeClipThreshold": 20, 
        "simpleClipThreshold": 20, 
        "minAdapterLength": 4, 
        "keepBothReads": "true"
    }, 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/reads1": {
        "basename": "S1_R1.fastq.gz", 
        "nameroot": "S1_R1.fastq", 
        "nameext": ".gz", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz", 
        "class": "File", 
        "size": 2678369
    }, 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/end_mode": "PE", 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/nthreads": 1, 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/reads2": {
        "basename": "S1_R2.fastq.gz", 
        "nameroot": "S1_R2.fastq", 
        "nameext": ".gz", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz", 
        "class": "File", 
        "size": 2746137
    }
}
[job step trim] evaluated job input to {
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/illuminaClip": {
        "adapters": {
            "class": "File", 
            "location": "file:///stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa"
        }, 
        "seedMismatches": 1, 
        "palindromeClipThreshold": 20, 
        "simpleClipThreshold": 20, 
        "minAdapterLength": 4, 
        "keepBothReads": "true"
    }, 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/reads1": {
        "format": "http://edamontology.org/format_1930", 
        "basename": "S1_R1.fastq.gz", 
        "nameroot": "S1_R1.fastq", 
        "nameext": ".gz", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz", 
        "class": "File", 
        "size": 2678369
    }, 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/end_mode": "PE", 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/nthreads": 8, 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl#trim/reads2": {
        "format": "http://edamontology.org/format_1930", 
        "basename": "S1_R2.fastq.gz", 
        "nameroot": "S1_R2.fastq", 
        "nameext": ".gz", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz", 
        "class": "File", 
        "size": 2746137
    }
}
[step trim] start
[job trim] initializing from file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/tools/trimmomatic.cwl as part of step trim
[job trim] {
    "nthreads": 8, 
    "illuminaClip": {
        "adapters": {
            "class": "File", 
            "location": "file:///stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa"
        }, 
        "seedMismatches": 1, 
        "palindromeClipThreshold": 20, 
        "simpleClipThreshold": 20, 
        "minAdapterLength": 4, 
        "keepBothReads": "true"
    }, 
    "reads2": {
        "format": "http://edamontology.org/format_1930", 
        "basename": "S1_R2.fastq.gz", 
        "nameroot": "S1_R2.fastq", 
        "nameext": ".gz", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz", 
        "class": "File", 
        "size": 2746137
    }, 
    "reads1": {
        "format": "http://edamontology.org/format_1930", 
        "basename": "S1_R1.fastq.gz", 
        "nameroot": "S1_R1.fastq", 
        "nameext": ".gz", 
        "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz", 
        "class": "File", 
        "size": 2678369
    }, 
    "end_mode": "PE"
}
[job trim] path mappings is {
    "file:///stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa": [
        "/stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa", 
        "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stg1c25dd07-8d1c-444a-bf77-30bc58e43107/TruSeq3-PE.fa", 
        "File", 
        true
    ], 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz": [
        "/stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz", 
        "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stg1bb23088-b117-4be7-853e-2f65d472c0dd/S1_R2.fastq.gz", 
        "File", 
        true
    ], 
    "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz": [
        "/stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz", 
        "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stge58b1ea3-9f2b-4644-97a9-5f2706585424/S1_R1.fastq.gz", 
        "File", 
        true
    ]
}
[job trim] command line bindings is [
    {
        "position": [
            -1000000, 
            0
        ], 
        "datum": "java"
    }, 
    {
        "position": [
            -1000000, 
            1
        ], 
        "datum": "org.usadellab.trimmomatic.Trimmomatic"
    }, 
    {
        "position": [
            1, 
            "java_opts"
        ], 
        "shellQuote": false, 
        "datum": null
    }, 
    {
        "position": [
            3, 
            "end_mode"
        ], 
        "datum": "PE"
    }, 
    {
        "valueFrom": "$(inputs.reads1.nameroot).log", 
        "prefix": "-trimlog", 
        "position": [
            4, 
            0
        ]
    }, 
    {
        "position": [
            4, 
            "nthreads"
        ], 
        "prefix": "-threads", 
        "datum": 8
    }, 
    {
        "prefix": "-phred", 
        "separate": false, 
        "position": [
            4, 
            "phred"
        ], 
        "datum": "64"
    }, 
    {
        "position": [
            5, 
            "reads1"
        ], 
        "datum": {
            "format": "http://edamontology.org/format_1930", 
            "basename": "S1_R1.fastq.gz", 
            "nameroot": "S1_R1.fastq", 
            "nameext": ".gz", 
            "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R1.fastq.gz", 
            "path": "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stge58b1ea3-9f2b-4644-97a9-5f2706585424/S1_R1.fastq.gz", 
            "dirname": "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stge58b1ea3-9f2b-4644-97a9-5f2706585424", 
            "class": "File", 
            "size": 2678369
        }
    }, 
    {
        "position": [
            6, 
            "reads2"
        ], 
        "datum": {
            "format": "http://edamontology.org/format_1930", 
            "basename": "S1_R2.fastq.gz", 
            "nameroot": "S1_R2.fastq", 
            "nameext": ".gz", 
            "location": "file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/test/data/S1_R2.fastq.gz", 
            "path": "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stg1bb23088-b117-4be7-853e-2f65d472c0dd/S1_R2.fastq.gz", 
            "dirname": "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stg1bb23088-b117-4be7-853e-2f65d472c0dd", 
            "class": "File", 
            "size": 2746137
        }
    }, 
    {
        "valueFrom": "$(inputs.reads1.nameroot).trimmed.fastq", 
        "position": [
            7, 
            1
        ]
    }, 
    {
        "valueFrom": "${\n  if (inputs.end_mode == \"PE\" && inputs.reads1) {\n    return inputs.reads1.nameroot + '.trimmed.unpaired.fastq';\n  } else {\n    return null;\n  }\n}\n", 
        "position": [
            8, 
            2
        ]
    }, 
    {
        "valueFrom": "${\n  if (inputs.end_mode == \"PE\" && inputs.reads2) {\n    return inputs.reads2.nameroot + '.trimmed.fastq';\n  } else {\n    return null;\n  }\n}\n", 
        "position": [
            9, 
            3
        ]
    }, 
    {
        "valueFrom": "${\n  if (inputs.end_mode == \"PE\" && inputs.reads2) {\n    return inputs.reads2.nameroot + '.trimmed.unpaired.fastq';\n  } else {\n    return null;\n  }\n}\n", 
        "position": [
            10, 
            4
        ]
    }, 
    {
        "valueFrom": "ILLUMINACLIP:$(inputs.illuminaClip.adapters.path):$(self.seedMismatches):$(self.palindromeClipThreshold):$(self.simpleClipThreshold):$(self.minAdapterLength):$(self.keepBothReads)\n", 
        "position": [
            11, 
            "illuminaClip"
        ], 
        "datum": {
            "adapters": {
                "class": "File", 
                "location": "file:///stornext/System/data/apps/trimmomatic/trimmomatic-0.36/adapters/TruSeq3-PE.fa", 
                "basename": "TruSeq3-PE.fa", 
                "nameroot": "TruSeq3-PE", 
                "nameext": ".fa", 
                "path": "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stg1c25dd07-8d1c-444a-bf77-30bc58e43107/TruSeq3-PE.fa", 
                "dirname": "/stornext/HPCScratch/home/thomas.e/tmp/tmpuZP2X2/stg1c25dd07-8d1c-444a-bf77-30bc58e43107"
            }, 
            "seedMismatches": 1, 
            "palindromeClipThreshold": 20, 
            "simpleClipThreshold": 20, 
            "minAdapterLength": 4, 
            "keepBothReads": "true"
        }
    }, 
    {
        "position": [
            12, 
            "tophred33"
        ], 
        "prefix": "TOPHRED33", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            12, 
            "tophred64"
        ], 
        "prefix": "TOPHRED64", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            13, 
            "crop"
        ], 
        "prefix": "CROP:", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            13, 
            "headcrop"
        ], 
        "prefix": "HEADCROP:", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            14, 
            "leading"
        ], 
        "prefix": "LEADING:", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            14, 
            "trailing"
        ], 
        "prefix": "TRAILING:", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            15, 
            "maxinfo"
        ], 
        "valueFrom": "MAXINFO:$(self.targetLength):$(strictness)\n", 
        "datum": null
    }, 
    {
        "position": [
            15, 
            "slidingwindow"
        ], 
        "valueFrom": "'SLIDINGWINDOW:'$(self.windowSize)':'$(self.requiredQuality)\n", 
        "datum": null
    }, 
    {
        "position": [
            100, 
            "minlen"
        ], 
        "prefix": "MINLEN:", 
        "separate": false, 
        "datum": null
    }, 
    {
        "position": [
            101, 
            "avgqual"
        ], 
        "prefix": "AVGQUAL:", 
        "separate": false, 
        "datum": null
    }
]
Exception on step 'trim'
[step trim] Cannot make job: :1:1: Expression evaluation error:
:1:1: self is a NoneType, cannot index on string 'targetLength'

Traceback (most recent call last):
  File "/home/thomas.e/.local/lib/python2.7/site-packages/cwltool/workflow.py", line 480, in job
    for newjob in step.iterable:
  File "/home/thomas.e/.local/lib/python2.7/site-packages/cwltool/workflow.py", line 427, in try_make_job
    for j in jobs:
  File "/home/thomas.e/.local/lib/python2.7/site-packages/cwltool/workflow.py", line 263, in job
    for j in self.step.job(joborder, output_callback, **kwargs):
  File "/home/thomas.e/.local/lib/python2.7/site-packages/cwltool/workflow.py", line 806, in job
    **kwargs):
  File "/home/thomas.e/.local/lib/python2.7/site-packages/cwltool/draft2tool.py", line 478, in job
    arg = builder.generate_arg(b)
  File "/home/thomas.e/.local/lib/python2.7/site-packages/cwltool/builder.py", line 199, in generate_arg
    value = self.do_eval(binding["valueFrom"], context=value)
  File "/home/thomas.e/.local/lib/python2.7/site-packages/schema_salad/sourceline.py", line 152, in __exit__
    raise self.makeError(six.text_type(exc_value))
WorkflowException: :1:1: Expression evaluation error:
:1:1: self is a NoneType, cannot index on string 'targetLength'
[workflow pdx-pl.cwl] completed permanentFail
Removing intermediate output directory /home/thomas.e/tmp/tmp9QQs3v
{
    "secondary_specific": null, 
    "secondary_multi": null, 
    "mouse-aligned": null, 
    "human-aligned": null, 
    "human-compress": null, 
    "primary_specific": null, 
    "unassigned": null, 
    "primary_multi": null, 
    "varscan": null, 
    "human-index": null, 
    "rename_reads1_trimmed_file": null, 
    "unresolved": null, 
    "trim-logs": null, 
    "reads1_trimmed_unpaired_file": null, 
    "reads2_trimmed_unpaired_file": null, 
    "human-mpileup": null, 
    "gridss": null, 
    "rename_reads2_trimmed_paired_file": null, 
    "platypus-vcf": null, 
    "human-sorted": null
}
Final process status is permanentFail

Your Environment

• cwltool version: Check using cwltool --version

$ cwltool --version
/home/thomas.e/.local/bin/cwltool 1.0.20170803160545

[evan-wehi]

@mr-c Ok, thanks for fixing this. I will integrate this into my WF soon.

[mr-c]

Turns out cwltool was not fully following the spec, now it is. See https://github.com/common-workflow-language/workflows/pull/139 for the sorts of changes you’ll need