updating READMEs

.github/workflows/main.yml

@@ -18,15 +18,15 @@ jobs:
  run: |
  pip3 install jsonschema
  pip3 install requests
- - name: Check validity of traces
+ - name: Check validity of instances
  run: |
- find . -type f -name "*.json" > traces.txt && err=0
+ find . -type f -name "*.json" > instances.txt && err=0
  git clone https://github.com/wfcommons/workflow-schema
  err_report() {
- echo "Error on trace file $1"
+ echo "Error on instance file $1"
  }
- trap 'err_report ${trace_file}' ERR;
- for trace_file in `cat traces.txt`; do
- python3 ./workflow-schema/wfcommons-validator.py -d ${trace_file};
+ trap 'err_report ${instance_file}' ERR;
+ for instance_file in `cat instances.txt`; do
+ python3 ./workflow-schema/wfcommons-validator.py -d ${instance_file};
  echo "";
  done

1000genome/README.md

@@ -1,7 +1,7 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/wordpress/wp-content/uploads/2015/12/logo-dark.png" width=200 style="float: right" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
-# Execution Traces for 1000Genome Workflow
+# Execution Instances for 1000Genome Workflow
 
 ## Workflow Description
 
@@ -42,14 +42,14 @@ performance metrics can be found in the following research publication:
  Future Generation Computer Systems, 95, 615–628.
  https://doi.org/10.1016/j.future.2019.01.015.
 
-## Execution Traces
+## Execution Instances
 
-Execution traces are formatted according to the
+Execution instances are formatted according to the
 [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) for
-describing workflow executions. Execution traces from different computing
+describing workflow executions. Execution instances from different computing
 platforms are organized into sub-folders.
 
-Trace files are named using the following convention:
+Instance files are named using the following convention:
 `1000genome-<COMPUTE_PLATFORM>-<NUM_CH>ch-<NUM_SEQ>-<RUN_ID>.json`, where:
 
 - `<COMPUTE_PLATFORM>`: The compute platform where the actual Pegasus workflow

cycles/README.md

@@ -1,7 +1,7 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/wordpress/wp-content/uploads/2015/12/logo-dark.png" width=200 style="float: right" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
-# Execution Traces for Cycles Workflow
+# Execution Instances for Cycles Workflow
 
 ## Workflow Description
 
@@ -40,14 +40,14 @@ performance metrics can be found in the following research publication:
  Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery
  (BTSD) (pp. 4545–4552). https://doi.org/10.1109/BigData47090.2019.9006107
 
-## Execution Traces
+## Execution Instances
 
-Execution traces are formatted according to the
+Execution instances are formatted according to the
 [WfCommons JSON format](https://github.com/wfcommons/workflow-schema)
-for describing workflow executions. Execution traces from different
+for describing workflow executions. Execution instances from different
 computing platforms are organized into sub-folders.
 
-Trace files are named using the following convention:
+Instance files are named using the following convention:
 `cycles-<COMPUTE_PLATFORM>-<LOCATIONS>-<CROPS>-<PARAMS>-<RUN_ID>.json`, where:
 
 - `<COMPUTE_PLATFORM>`: The compute platform where the actual Pegasus workflow

epigenomics/README.md

@@ -1,7 +1,7 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/wordpress/wp-content/uploads/2015/12/logo-dark.png" width=200 style="float: right" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
-# Execution Traces for Epigenomics Workflow
+# Execution Instances for Epigenomics Workflow
 
 ## Workflow Description
 
@@ -38,14 +38,14 @@ performance metrics can be found in the following research publication:
  "Characterizing and Profiling Scientific Workflows," Future Generation
  Computer Systems, vol. 29, iss. 3, pp. 682-692, 2013.
 
-## Execution Traces
+## Execution Instances
 
-Execution traces are formatted according to the
+Execution instances are formatted according to the
 [WfCommons JSON format](https://github.com/wfcommons/workflow-schema)
-for describing workflow executions. Execution traces from different
+for describing workflow executions. Execution instances from different
 computing platforms are organized into sub-folders.
 
-Trace files are named using the following convention:
+Instance files are named using the following convention:
 `epigenomics-<COMPUTE_PLATFORM>-<DATASET>-<NUM_SEQ>-<BIN_SIZE>-<RUN_ID>.json`, where:
 
 - `<COMPUTE_PLATFORM>`: The compute platform where the actual Pegasus workflow

montage/README.md

@@ -1,5 +1,5 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
 # Execution Instances for Montage Workflow
 

seismology/README.md

@@ -1,13 +1,13 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/wordpress/wp-content/uploads/2015/12/logo-dark.png" width=200 style="float: right" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
-# Execution Traces for Seismic Cross Correlation Workflow
+# Execution Instances for Seismic Cross Correlation Workflow
 
 ## Workflow Description
 
 The Seismic Cross Correlation workflow represents a common data-intensive
 analysis pattern used by many seismologists. The workflow preprocesses and
-cross-correlates traces (sequences of measurements of acceleration in three
+cross-correlates instances (sequences of measurements of acceleration in three
 dimensions) from multiple seismic stations.
  The workflow is composed of two different tasks:
 
@@ -34,14 +34,14 @@ publication:
  science. In 7th International Workshop on Data-Intensive Computing in the
  Clouds (pp. 1–8). https://doi.org/10.1109/DataCloud.2016.004
 
-## Execution Traces
+## Execution Instances
 
-Execution traces are formatted according to the
+Execution instances are formatted according to the
 [WfCommons JSON format](https://github.com/wfcommons/workflow-schema)
-for describing workflow executions. Execution traces from different
+for describing workflow executions. Execution instances from different
 computing platforms are organized into sub-folders.
 
-Trace files are named using the following convention:
+Instance files are named using the following convention:
 `seismology-<COMPUTE_PLATFORM>-<NUM_PAIRS>p-<RUN_ID>.json`, where:
 
 - `<COMPUTE_PLATFORM>`: The compute platform where the actual Pegasus workflow

soykb/README.md

@@ -1,7 +1,7 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/wordpress/wp-content/uploads/2015/12/logo-dark.png" width=200 style="float: right" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
-# Execution Traces for Soybean Workflow (SoyKB)
+# Execution Instances for Soybean Workflow (SoyKB)
 
 ## Workflow Description
 
@@ -45,14 +45,14 @@ performance metrics can be found in the following research publication:
  workflow and browser in SoyKB,” BMC Bioinformatics, vol. 17, iss. 13, p.
  337, 2016. https://doi.org/10.1186/s12859-016-1227-y
 
-## Execution Traces
+## Execution Instances
 
-Execution traces are formatted according to the
+Execution instances are formatted according to the
 [WfCommons JSON format](https://github.com/wfcommons/workflow-schema)
-for describing workflow executions. Execution traces from different
+for describing workflow executions. Execution instances from different
 computing platforms are organized into sub-folders.
 
-Trace files are named using the following convention:
+Instance files are named using the following convention:
 `soykb-<COMPUTE_PLATFORM>-<NUM_FASTQ>-<NUM_CH>-<RUN_ID>.json`, where:
 
 - `<COMPUTE_PLATFORM>`: The compute platform where the actual Pegasus workflow

srasearch/README.md

@@ -1,7 +1,7 @@
 <img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" />
-<img src="https://pegasus.isi.edu/wordpress/wp-content/uploads/2015/12/logo-dark.png" width=200 style="float: right" />
+<img src="https://pegasus.isi.edu/documentation/_static/pegasus_circular_white_logo.png" width="100"/>
 
-# Execution Traces for SRA Search Workflow
+# Execution Instances for SRA Search Workflow
 
 ## Workflow Description
 
@@ -24,14 +24,14 @@ The figure below shows an overview of the SRA Search workflow structure:
 
 <img src="docs/images/srasearch.png?raw=true" width="600">
 
-## Execution Traces
+## Execution Instances
 
-Execution traces are formatted according to the
+Execution instances are formatted according to the
 [WfCommons JSON format](https://github.com/wfcommons/workflow-schema) for
-describing workflow executions. Execution traces from different computing
+describing workflow executions. Execution instances from different computing
 platforms are organized into sub-folders.
 
-Trace files are named using the following convention:
+Instance files are named using the following convention:
 `srasearch-<COMPUTE_PLATFORM>-<ACCESSION_LIST_SIZE>-<RUN_ID>.json`, where:
 
 - `<COMPUTE_PLATFORM>`: The compute platform where the actual Pegasus workflow