cwlVersion: v1.0
class: Workflow
inputs:
  inp: File
  ex: string

outputs:
  classout:
    type: File
    outputSource: compile/classfile

steps:
  untar:
    run: tar-param.cwl
    in:
      tarfile: inp
      extractfile: ex
    out: [example_out]

  compile:
    run: arguments.cwl
    in:
      src: untar/example_out
    out: [classfile]

cwlVersion: v1.0
class: Workflow

inputs:
  toConvert: File


outputs:
  converted: 
    type: File
    outputSource: convertMethylation/converted
  combined: 
    type: File
    outputSource: mergeSymmetric/combined


steps:
  convertMethylation:
    run: interconverter.cwl
    in:
      toConvert: toConvert
    out: [converted]
  mergeSymmetric:
    run: symmetriccpgs.cwl
    in:
      toCombine: convertMethylation/converted
    out: [combined]

cwlVersion: v1.0
class: CommandLineTool
baseCommand: interconverter.sh
hints:
  - class: DockerRequirement
    dockerPull: "quay.io/neksa/screw-tool"
arguments: ["-d", $(runtime.outdir)]
inputs:
  toConvert:
    type: File
    inputBinding:
      prefix: -i
outputs:
  converted:
    type: File
    outputBinding:
      glob: "*.meth"

cwlVersion: v1.0
class: CommandLineTool
baseCommand: symmetriccpgs.sh
arguments: ["-d", $(runtime.outdir)]
hints:
  - class: DockerRequirement
    dockerPull: "quay.io/neksa/screw-tool"

inputs:
  toCombine:
    type: File
    inputBinding:
      prefix: -i
outputs:
  combined:
    type: File
    outputBinding:
      glob: "*.sym"

cwlVersion: v1.0
class: Workflow
label: EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

requirements:
 - class: SubworkflowFeatureRequirement
 - class: SchemaDefRequirement
   types: 
    - $import: ../tools/FragGeneScan-model.yaml
    - $import: ../tools/trimmomatic-sliding_window.yaml
    - $import: ../tools/trimmomatic-end_mode.yaml
    - $import: ../tools/trimmomatic-phred.yaml

inputs:
  reads:
    type: File
    format: edam:format_1930  # FASTQ

outputs:
  processed_sequences:
    type: File
    outputSource: clean_fasta_headers/sequences_with_cleaned_headers

steps:
  trim_quality_control:
    doc: |
      Low quality trimming (low quality ends and sequences with < quality scores
      less than 15 over a 4 nucleotide wide window are removed)
    run: ../tools/trimmomatic.cwl
    in:
      reads1: reads
      phred: { default: '33' }
      leading: { default: 3 }
      trailing: { default: 3 }
      end_mode: { default: SE }
      minlen: { default: 100 }
      slidingwindow:
        default:
          windowSize: 4
          requiredQuality: 15
    out: [reads1_trimmed]

  convert_trimmed-reads_to_fasta:
    run: ../tools/fastq_to_fasta.cwl
    in:
      fastq: trim_quality_control/reads1_trimmed
    out: [ fasta ]

  clean_fasta_headers:
    run: ../tools/clean_fasta_headers.cwl
    in:
      sequences: convert_trimmed-reads_to_fasta/fasta
    out: [ sequences_with_cleaned_headers ]


$namespaces:
 edam: http://edamontology.org/
 s: http://schema.org/
$schemas:
 - http://edamontology.org/EDAM_1.16.owl
 - https://schema.org/docs/schema_org_rdfa.html

s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"

FROM ubuntu:14.04
MAINTAINER Stian Soiland-Reyes <soiland-reyes@cs.manchester.ac.uk>

# Install apache/PHP for REST API
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
	apache2 php5 memcached php5-memcached php5-memcache php5-curl \
        supervisor \
        unzip wget 
RUN a2enmod rewrite

RUN rm -rf /var/www/html
#Install Linked Data API
RUN wget https://github.com/openphacts/OPS_LinkedDataApi/archive/1.5.0.zip -O /tmp/api.zip && \
    cd /tmp && \
    unzip api.zip && \
    mv /tmp/OPS* /var/www/html

RUN sed -i '/<\/VirtualHost/ i\ <Directory /var/www/html/>\n  AllowOverride All\n </Directory>' /etc/apache2/sites-enabled/000-default.conf
#RUN cat /etc/apache2/apache2.conf | tr "\n" "|||" | \
#      sed 's,\(<Directory /var/www/html/>[^<]*\)AllowOverride None\([^<]*</Directory>\),\1AllowOverride All\2,' | \
#      sed 's/|||/n/g' >/tmp/apache2 && \
#    mv /tmp/apache2 /etc/apache2/apache2.conf
RUN mkdir /var/www/html/logs /var/www/html/cache && \
    chmod 777 /var/www/html/logs /var/www/html/cache && \
    chown -R www-data:www-data /var/www/html

#!/usr/bin/env cwl-runner

cwlVersion: v1.0

class: CommandLineTool

baseCommand: ["gmx", "pdb2gmx"]

arguments: ["-o", "processed.gro"]

inputs:
  pdb:
    type: string
    inputBinding:
      prefix: -f
  water:
    type: File
    inputBinding:
      prefix: -water
    default: spce

outputs:
  processed_gro:
    type: File
    outputBinding:
      glob: processed.gro

cwlVersion: v1.0
class: CommandLineTool
baseCommand: node
hints:
  DockerRequirement:
    dockerPull: gromacs/gromacs:2018.4

class: CommandLineTool
hints:
  SoftwareRequirement:
    packages:
      samtools:
        version: [ "0.1.19" ]

baseCommand: ["samtools", "index"]
#..

module load samtools/0.1.19

apt-get install samtools=0.1.19*

conda install samtools=0.1.19

hints:
  SoftwareRequirement:
    packages:
    - package: gromacs
      version:
      - '2018.4'
      specs:
      - https://packages.debian.org/gromacs
      - https://anaconda.org/bioconda/gromacs
      - https://bio.tools/gromacs
      - https://identifiers.org/rrid/RRID:SCR_014565
      - https://hpc.example.edu/modules/gromacs/2018.4
  DockerRequirement:
    dockerPull: gromacs/gromacs:2018.4

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo

requirements:
  InlineJavascriptRequirement: {}

inputs: []
outputs:
  example_out:
    type: stdout
stdout: output.txt
arguments:
  - prefix: -A
    valueFrom: $(1+1)
  - prefix: -B
    valueFrom: $("/foo/bar/baz".split('/').slice(-1)[0])
  - prefix: -C
    valueFrom: |
      ${
        var r = [];
        for (var i = 10; i >= 1; i--) {
          r.push(i);
        }
        return r;
      }

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool

requirements:
  DockerRequirement:
    dockerPull: lukasheinrich/dummyanalysis
  ShellCommandRequirement: {}

baseCommand: /bin/bash

arguments:
  - valueFrom: |
      source /usr/local/bin/thisroot.sh
      cat $(runtime.outdir)/input_list | xargs hadd merged.root
    prefix: -c
   
# (..)

#!/usr/bin/env cwl-runner
#
# Example score submission file
#
cwlVersion: v1.0
class: CommandLineTool

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: score.py
        entry: |
          #!/usr/bin/env python
          import synapseclient
          import argparse
          import os
          import json
          parser = argparse.ArgumentParser()
          parser.add_argument("-f", "--submissionfile", required=True, help="Submission File")
          # ..
          args = parser.parse_args()
          score = 3
          prediction_file_status = "SCORED"
          result = {'score':score, 'prediction_file_status':prediction_file_status}
          with open(args.results, 'w') as o:
            o.write(json.dumps(result))

baseCommand: python

arguments:
  - valueFrom: score.py
  - valueFrom: $(inputs.inputfile.path)
    prefix: -f


inputs:
  - id: inputfile
    type: File


outputs:
  - id: results
    type: File
    outputBinding:
      glob: results.json

(venv3) stain@biggie:~/src/cwlprov-py/test/nested-cwlprov-0.3.0$ cwlprov run
2018-08-08 22:44:06.573330 Flow 39408a40-c1c8-4852-9747-87249425be1e [ Run of workflow/packed.cwl#main 
2018-08-08 22:44:06.691722 Step 4f082fb6-3e4d-4a21-82e3-c685ce3deb58   Run of workflow/packed.cwl#main/create-tar  (0:00:00.010133)
2018-08-08 22:44:06.702976 Step 0cceeaf6-4109-4f08-940b-f06ac959944a * Run of workflow/packed.cwl#main/compile  (unknown duration)
2018-08-08 22:44:12.680097 Flow 39408a40-c1c8-4852-9747-87249425be1e ] Run of workflow/packed.cwl#main  (0:00:06.106767)
Legend:
[ Workflow start
* Nested provenance, use UUID to explore: cwlprov run 0cceeaf6-4109-4f08-940b-f06ac959944a
] Workflow end

(venv3) stain@biggie:~/src/cwlprov-py/test/nested-cwlprov-0.3.0$ cwlprov run 0cceeaf6-4109-4f08-940b-f06ac959944a
2018-08-08 22:44:06.607210 Flow 0cceeaf6-4109-4f08-940b-f06ac959944a [ Run of workflow/packed.cwl#main 
2018-08-08 22:44:06.707070 Step 83752ab4-8227-4d4a-8baa-78376df34aed   Run of workflow/packed.cwl#main/untar  (0:00:00.008149)
2018-08-08 22:44:06.718554 Step f56d8478-a190-4251-84d9-7f69fe0f6f8b   Run of workflow/packed.cwl#main/argument  (0:00:00.532052)
2018-08-08 22:44:07.251588 Flow 0cceeaf6-4109-4f08-940b-f06ac959944a ] Run of workflow/packed.cwl#main  (0:00:00.644378)
Legend:
[ Workflow start
] Workflow end

stain@biggie:~/src/cwlprov-py/test/nested-cwlprov-0.3.0$ cwlprov outputs 4f082fb6-3e4d-4a21-82e3-c685ce3deb58 --format=files
Output tar:
data/c0/c0fd5812fe6d8d91fef7f4f1ba3a462500fce0c5

stain@biggie:~/src/cwlprov-py/test/nested-cwlprov-0.3.0$ tar tfv `cwlprov -q outputs 4f082fb6-3e4d-4a21-82e3-c685ce3deb58 --format=files`
-rw-r--r-- stain/stain     115 2018-08-08 23:44 Hello.java

$ cwlprov --help
usage: cwlprov [-h] [--version] [--directory DIRECTORY] [--relative]
            [--absolute] [--output OUTPUT] [--verbose] [--quiet] [--hints]
            [--no-hints]
            {validate,info,who,prov,inputs,outputs,run,runs,rerun,derived,runtimes}
            ...

cwlprov explores Research Objects containing provenance of Common Workflow
Language executions. <https://w3id.org/cwl/prov/>

commands:
{validate,info,who,prov,inputs,outputs,run,runs,rerun,derived,runtimes}
    validate            Validate the CWLProv Research Object
    info                show research object Metadata
    who                 show Who ran the workflow
    prov                export workflow execution Provenance in PROV format
    inputs              list workflow/step Input files/values
    outputs             list workflow/step Output files/values
    run                 show workflow Execution log
    runs                List all workflow executions in RO
    rerun               Rerun a workflow or step
    derived             list what was Derived from a data item, based on
                        activity usage/generation
    runtimes            calculate average step execution Runtimes