Update to 1.0.20180622214234

.gitignore

@@ -1,2 +1,3 @@
 .DS_Store
 ._.DS_Store
+.idea

README.md

@@ -1,20 +1,32 @@
-# ChIP-Seq CWL pipeline from BioWardrobe 
+# ChIP-Seq-SE CWL pipeline from BioWardrobe 
 
-This workflow is a CWL version of a Python pipeline from BioWardrobe (Kartashov and Barski, 2015). It starts by using BowTie (Langmead et al., 2009) to perform alignment to a reference genome, resulting in an unsorted SAM file. The SAM file is then sorted and indexed with samtools (Li et al., 2009) to obtain a BAM file and a BAI index. Next MACS2 (Zhang et al., 2008) is used to call peaks and to estimate fragment size. In the last few steps, the coverage by estimated fragments is calculated from the BAM file and is reported in bigWig format. The pipeline also reports statistics, such as read quality, peak number and base frequency, and other troubleshooting information using tools such as [fastx-toolkit](http://hannonlab.cshl.edu/fastx_toolkit/) and [bamtools](https://github.com/pezmaster31/bamtools).
+This workflow is a CWL version of a Python pipeline from BioWardrobe (Kartashov and Barski, 2015).
+It starts by extracting input FASTQ file (if it was compressed). Next step runs
+BowTie (Langmead et al., 2009) to perform alignment to a reference genome,
+resulting in an unsorted SAM file. The SAM file is then sorted and indexed with Samtools
+(Li et al., 2009) to obtain a BAM file and a BAI index. Next MACS2 (Zhang et al., 2008)
+is used to call peaks and to estimate fragment size. In the last few steps, the coverage
+by estimated fragments is calculated from the BAM file and is reported in bigWig format.
+The pipeline also reports statistics, such as read quality, peak number and base frequency,
+and other troubleshooting information using tools such as
+[fastx-toolkit](http://hannonlab.cshl.edu/fastx_toolkit/) and
+[bamtools](https://github.com/pezmaster31/bamtools).
 
-This workflow (v0.0.2) is being used for GA4GH/DREAM challenge (phase 2).
+This workflow (v0.0.2) is being used for
+[GA4GH-DREAM Workflow Execution Challenge](https://www.synapse.org/#!Synapse:syn8507133/wiki/415976).
 
-The pipeline scheme is available in the Wiki.
-
-To download workflow with testing input data use
+**To download workflow with the testing input data run the following command**
 ```
 git clone --recursive https://github.com/Barski-lab/ga4gh_challenge.git
-```
-It will clone submodule [ga4gh_challenge_data](https://github.com/michael-kotliar/ga4gh_challenge_data)
-into `data`folder.
-Uncompress input FASTQ file using
-```
 cd ga4gh_challenge/data
 ./prepare_inputs.sh
 ```
-> tested with cwltool==1.0.20180116213856
+It will also clone submodule [ga4gh_challenge_data](https://github.com/michael-kotliar/ga4gh_challenge_data)
+into the *data* folder and uncompress input FASTQ file.
+
+
+![Workflow scheme](docs/workflow_sheme.png)
+Pipeline scheme generated by [Rabix Composer](http://rabix.io/).
+
+
+*tested with cwltool==1.0.20180622214234*

biowardrobe_chipseq_se.cwl

@@ -4,8 +4,10 @@ class: Workflow
 
 requirements:
   - class: SubworkflowFeatureRequirement
+  - class: ScatterFeatureRequirement
   - class: StepInputExpressionRequirement
   - class: InlineJavascriptRequirement
+  - class: MultipleInputFeatureRequirement
 
 
 inputs:
@@ -86,7 +88,6 @@ inputs:
     doc: "Number of threads for those steps that support multithreading"
     label: "Number of threads"
 
-
 outputs:
 
   bigwig:
@@ -215,30 +216,24 @@ outputs:
     doc: "fragment, calculated fragment, islands count from MACS2 results"
     outputSource: macs2_callpeak/macs2_stat_file
 
-  fastq_compressed:
-    type: File
-    label: "Compressed FASTQ"
-    doc: "bz2 compressed FASTQ file"
-    outputSource: bzip/output_file
-
 steps:
 
+  extract_fastq:
+    run: ./tools/extract-fastq.cwl
+    in:
+      compressed_file: fastq_file
+    out: [fastq_file]
+
   fastx_quality_stats:
     run: ./tools/fastx-quality-stats.cwl
     in:
-      input_file: fastq_file
+      input_file: extract_fastq/fastq_file
     out: [statistics_file]
 
-  bzip:
-    run: ./tools/bzip2-compress.cwl
-    in:
-      input_file: fastq_file
-    out: [output_file]
-
   bowtie_aligner:
     run: ./tools/bowtie-alignreads.cwl
     in:
-      upstream_filelist: fastq_file
+      upstream_filelist: extract_fastq/fastq_file
       indices_folder: indices_folder
       clip_3p_end: clip_3p_end
       clip_5p_end: clip_5p_end
@@ -323,7 +318,7 @@ steps:
       - macs2_fragments_calculated
 
   bam_to_bigwig:
-    run: ./workflows/bam-bedgraph-bigwig.cwl
+    run: ./subworkflows/bam-bedgraph-bigwig.cwl
     in:
       bam_file: samtools_sort_index_after_rmdup/bam_bai_pair
       chrom_length_file: chrom_length
@@ -411,33 +406,17 @@ s:creator:
         - id: http://orcid.org/0000-0002-6486-3898
 
 doc: |
-  Current workflow is used to run CHIP-Seq basic analysis with single-end input FASTQ file.
+  The workflow is used to run CHIP-Seq basic analysis with single-end input FASTQ file.
   In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality
-  statistics of the input FASTQ file, reads coverage in a form of BigWig file, peaks calling
+  statistics of the input FASTQ file, reads coverage in a form of bigWig file, peaks calling
   data in a form of narrowPeak or broadPeak files.
 
 s:about: |
-  Current workflow is used to run CHIP-Seq basic analysis with single-end input FASTQ file.
-  In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality
-  statistics of the input FASTQ file, reads coverage in a form of BigWig file, peaks calling
-  data in a form of narrowPeak or broadPeak files.
-  Workflow starts with running fastx_quality_stats (Step fastx_quality_stats) from FASTX-Toolkit
-  to calculate quality statistics for input FASTQ file. At the same time (Step bowtie_aligner)
-  Bowtie is used to align reads from input FASTQ file to reference genome. The output of this step
-  is unsorted SAM file which is being sorted and indexed by samtools sort and samtools index
-  (Step samtools_sort_index). Depending on workflow’s input parameters indexed the sorted BAM file
-  could be processed by samtools rmdup (Step samtools_rmdup) to remove all possible read duplicates.
-  In a case when removing duplicates is not necessary the step returns original input BAM and BAI
-  files without any processing. If the duplicates were removed the following step
-  (Step samtools_sort_index_after_rmdup) reruns samtools sort and samtools index with BAM and BAI files,
-  if not - the step returns original unchanged input files. Right after that (Step macs2_callpeak)
-  macs2 callpeak performs peak calling. This step also calculates the number of islands and estimated
-  fragment size. If the last one is less that 80 (hardcoded in a workflow) macs2 callpeak is rerun again
-  with forced fixed fragment size value. If at the very beginning it was set in workflow
-  input parameters to run peak calling with fixed fragment size, macs2 peak calling is run only once.
-  The following step (Step bam_to_bigwig) is used to calculate read coverage on the base of input BAM file
-  and save it in bigWig format. For that purpose the mapped reads number is used as a scaling factor
-  by bedtools genomecov when it performs coverage calculation and saves it in BED format. The last one
-  is then being sorted and converted to bigWig format by bedGraphToBigWig tool from UCSC utilities.
-  The following two steps (Step island_intersect and average_tag_density) define the closest genes to
-  the islands received from macs2 peak calling and calculate average tag density.
+  The workflow is a CWL version of a Python pipeline from BioWardrobe (Kartashov and Barski, 2015).
+  It starts by extracting input FASTQ file (in case it was compressed). Next step runs BowTie
+  (Langmead et al., 2009) to perform alignment to a reference genome, resulting in an unsorted SAM file.
+  The SAM file is then sorted and indexed with samtools (Li et al., 2009) to obtain a BAM file and a BAI index.
+  Next MACS2 (Zhang et al., 2008) is used to call peaks and to estimate fragment size. In the last few steps,
+  the coverage by estimated fragments is calculated from the BAM file and is reported in bigWig format. The pipeline
+  also reports statistics, such as read quality, peak number and base frequency, and other troubleshooting information
+  using tools such as fastx-toolkit and bamtools.

biowardrobe_chipseq_se.yaml

@@ -19,5 +19,5 @@ remove_duplicates: false
 exp_fragment_size: 150
 force_fragment_size: false
 broad_peak: false
-threads: 8
+threads: 2
 genome_size: "1.2e8"

workflows/bam-bedgraph-bigwig.cwl → subworkflows/bam-bedgraph-bigwig.cwl

@@ -1,5 +1,3 @@
-#!/usr/bin/env cwl-runner
-
 cwlVersion: v1.0
 class: Workflow
 
@@ -88,14 +86,7 @@ steps:
         default: "-bg"
       split:
         source: split
-        valueFrom: |
-          ${
-            if (self == null){
-              return true;
-            } else {
-              return self;
-            }
-          }
+        default: true
       output_filename: bedgraph_filename
       pairchip: pairchip
       fragment_size: fragment_size
@@ -119,71 +110,4 @@ steps:
       bedgraph_file: sort_bedgraph/sorted_file
       chrom_length_file: chrom_length_file
       output_filename: bigwig_filename
-    out: [bigwig_file]
-
-$namespaces:
-  s: http://schema.org/
-
-$schemas:
-- http://schema.org/docs/schema_org_rdfa.html
-
-s:name: "bam-bedgraph-bigwig"
-s:downloadUrl: hhttps://raw.githubusercontent.com/Barski-lab/ga4gh_challenge/master/workflows/bam-bedgraph-bigwig.cwl
-s:codeRepository: https://github.com/Barski-lab/ga4gh_challenge
-s:license: http://www.apache.org/licenses/LICENSE-2.0
-
-s:isPartOf:
-  class: s:CreativeWork
-  s:name: Common Workflow Language
-  s:url: http://commonwl.org/
-
-s:creator:
-- class: s:Organization
-  s:legalName: "Cincinnati Children's Hospital Medical Center"
-  s:location:
-  - class: s:PostalAddress
-    s:addressCountry: "USA"
-    s:addressLocality: "Cincinnati"
-    s:addressRegion: "OH"
-    s:postalCode: "45229"
-    s:streetAddress: "3333 Burnet Ave"
-    s:telephone: "+1(513)636-4200"
-  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
-  s:department:
-  - class: s:Organization
-    s:legalName: "Allergy and Immunology"
-    s:department:
-    - class: s:Organization
-      s:legalName: "Barski Research Lab"
-      s:member:
-      - class: s:Person
-        s:name: Michael Kotliar
-        s:email: mailto:[email protected]
-        s:sameAs:
-        - id: http://orcid.org/0000-0002-6486-3898
-      - class: s:Person
-        s:name: Andrey Kartashov
-        s:email: mailto:[email protected]
-        s:sameAs:
-        - id: http://orcid.org/0000-0001-9102-5681
-
-doc: |
-  Workflow converts input BAM file into bigWig and bedGraph files
-
-s:about: |
-  Workflow converts input BAM file into bigWig and bedGraph files.
-
-  Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step).
-
-  If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split`
-  input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs.
-
-  `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for
-  `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is
-  implemented inside `bedtools-genomecov.cwl`.
-
-  `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name
-  for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided.
-
-  All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used
-  as subworkflow.
+    out: [bigwig_file]