ebi-metagenomics / workflow-is-cwl Goto Github PK

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

Common Workflow Language 4.36% Shell 0.26% Pep8 0.60% Roff 0.75% Dockerfile 0.05% HTML 93.98%

cwl-workflow common-workflow-language cwl workflow cwl-descriptions transdecoder diamond phmmer cwl-description marine

workflow-is-cwl's Introduction

ebi-metagenomics

Metagenomics at the EMBL-EBI

working name "MGportal"

Introduction

What's metagenomics?

The study of all genomes present in any given environment without the need for prior individual identification or amplification is termed metagenomics. For example, in its simplest form a metagenomic study might be the direct sequence results of DNA extracted from a bucket of sea water.

What is the EBI doing for metagenomic researchers?

The EBI resources of the European Nucleotide Archive (in particular Sequence Read Archive and EMBL-Bank), UniProt, InterPro, Ensembl Genomes and IntAct are all used for analysis by metagenomic researchers, but not in an integrated manner. We intend to provide a user friendly interface to these services, promoting their utility in the field of metagenomics. It will enable protein prediction, function analysis, comparison to complete reference genomes and metabolic pathway analysis.

This Project

The code here will include everything that has been generated to fulfill the above criteria, including the design of the web portal to submit and browse data.

MGportal is being developed as an open source project at EMBL European Bioinformatics Institute (EBI).

The web portal

The web portal is under development. Please visit us to see the latest version on http://www.ebi.ac.uk/metagenomics/.

workflow-is-cwl's People

Contributors

Stargazers

Watchers

Forkers

mr-c hmenager stain embl-ebi-tsi nathanielmki truwl

workflow-is-cwl's Issues

cwlexec: InterProScan5 result file is not mapped to the output binding

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"
  }
}

Trimmomatic: Add test inputs and expected outputs

Trinity: Add test inputs and expected outputs

Validating the complete assembly workflow

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

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]

BUSCO: Docker container doesn't write any results onto the local file system!

Container: comics/busco:3.0.2

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