This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts
Home Page: https://www.elixir-europe.org/
License: Apache License 2.0
Potential solution:
https://github.com/ola-t/interproscan-docker-cwl/blob/master/interproscan.cwl
Create a PR against: https://github.com/BioContainers/containers/tree/master/fastqc
Further information with the exact problem is following.
I am talking about: trinityrnaseq/trinityrnaseq:2.6.5
https://hub.docker.com/r/ycogne/transrate/
E.g. Set PATH appropriately.
Container: comics/busco:3.0.2
I'm working on the complete workflow validation. I've difficulties to figure out how to fix the issue below. Any idea ?
Tool definition failed validation: ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.cwl:155:5: Type property "['null', 'seq_type']" not a valid Avro schema: Union item must be a valid Avro schema: Could not make an Avro Schema object from seq_type.
Runned command :
cwltool --validate ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.cwl ../workflow-is-cwl-assembly/workflows/TranscriptomeAssembly-wf.test.job.paired-end.yaml
While running the annotation pipeline on a full transcriptome assembly, the assembly assessment step (BUSCO) failed, complaining about unsupported characters in the FASTA header
INFO Configuration loaded from /software/applications/busco/3.0.2/scripts/../config/config.ini
INFO Init tools...
INFO Check dependencies...
INFO Check input file...
ERROR The character '/' is present in the fasta header >MMETSP0795-doi:10.5281/zenodo.249982-Transcript_0, which will crash Reader. Please clean the header of your input file.
ERROR BUSCO analysis failed !
ERROR Check the logs, read the user guide, if you still need technical support, then please contact mailto:[email protected]
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"
}
}
For some reasons I cannot find the Trimmomatic biocontainer in Dockerhub
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