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EBI-Metagenomics / workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts
https://www.elixir-europe.org/
Apache License 2.0
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cwlexec: InterProScan5 result file is not mapped to the output binding #34

Open mscheremetjew opened 5 years ago

mscheremetjew commented 5 years ago

A reason for that could be that the I5 steps runs in scattered mode. Have a look at the produced JSON output (cwlexec) of the TranscriptsAnnotation workflow->i5Annotations:

{
  "coding_regions" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.cds",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.cds",
    "basename" : "test_transcripts.cleaned.fasta.transdecoder.cds",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned.fasta.transdecoder",
    "nameext" : ".cds",
    "checksum" : "sha1$a5c91d3096d3f691bb2fe751f589b3a5cceff905",
    "size" : 4883,
    "class" : "File"
  },
  "peptide_sequences" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.pep",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.pep",
    "basename" : "test_transcripts.cleaned.fasta.transdecoder.pep",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned.fasta.transdecoder",
    "nameext" : ".pep",
    "checksum" : "sha1$34b74df01848af46572d8a90749b5dc0a36519de",
    "size" : 1713,
    "class" : "File"
  },
  "reformatted_sequences" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.pep.reformatted_seqs",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.pep.reformatted_seqs",
    "basename" : "test_transcripts.cleaned.fasta.transdecoder.pep.reformatted_seqs",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned.fasta.transdecoder.pep",
    "nameext" : ".reformatted_seqs",
    "checksum" : "sha1$63510367a96fb7ac855bd87c5bd7ada924828ea9",
    "size" : 1713,
    "class" : "File"
  },
  "i5Annotations" : {
    "size" : 0,
    "secondaryFiles" : [ ],
    "class" : "File"
  },
  "cleaned_transcripts_file" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta",
    "basename" : "test_transcripts.cleaned.fasta",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned",
    "nameext" : ".fasta",
    "checksum" : "sha1$79fd0ed1d5b160b45f02f4ce627ac0bf2343411e",
    "size" : 15453,
    "format" : "http://edamontology.org/format_1929",
    "class" : "File"
  },
  "gff3_output" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.gff3",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.gff3",
    "basename" : "test_transcripts.cleaned.fasta.transdecoder.gff3",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned.fasta.transdecoder",
    "nameext" : ".gff3",
    "checksum" : "sha1$3b157e697608f1170664bc7acbf97466ee604b14",
    "size" : 741,
    "class" : "File"
  },
  "bed_output" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.bed",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.transdecoder.bed",
    "basename" : "test_transcripts.cleaned.fasta.transdecoder.bed",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned.fasta.transdecoder",
    "nameext" : ".bed",
    "checksum" : "sha1$733e6fcbb99cc4063e528a00bac66de9a2a9901c",
    "size" : 212,
    "class" : "File"
  },
  "diamond_matches" : {
    "location" : "file:///home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.diamond_matches",
    "path" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0/test_transcripts.cleaned.fasta.diamond_matches",
    "basename" : "test_transcripts.cleaned.fasta.diamond_matches",
    "dirname" : "/home/user/maxim/cwlexec-test/TranscriptsAnnotation-i5only-wf-426dab18-eb67-4274-8525-be8873ceeed0",
    "nameroot" : "test_transcripts.cleaned.fasta",
    "nameext" : ".diamond_matches",
    "checksum" : "sha1$0ba85f5d0453f9f74d68b94d8215ceb3223c1df1",
    "size" : 286,
    "class" : "File"
  }
}