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Commit e807faa9 authored by Felix Perez's avatar Felix Perez
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Update the documentation to include the new process.

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......@@ -13,6 +13,7 @@ The workflow `workflow/main.nf` has three processes:
- Convert all the text in the input files to uppercase
- Split the text so each word is on a separate line
- Remove all the empty lines generated from the split
- Sort, find and count the occurrence of unique words
This example uses SLURM to finish the calculation tasks. It may be slow due to the workload of the SLURM on BioHPC.
......@@ -70,7 +71,7 @@ The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the
When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to
`workflow/images/singularity/` for later use. In the workflow, the default configuration located in
`workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase,
toLines, and word count processes.
toLines, cleanlines, and word count processes.
### Vizapp containers
......
......@@ -5,10 +5,11 @@ in a text file.
## The Workflow
The workflow `workflow/main.nf` has three processes:
The workflow `workflow/main.nf` has four processes:
- Convert all the text in the input files to uppercase
- Split the text so each word is on a separate line
- Remove all empty lines generated from the previous output
- Sort, find and count the occurrence of unique words
This example uses SLURM to finish the calculation tasks. It may be slow due to the workload of the SLURM on BioHPC.
......@@ -63,10 +64,10 @@ astrocyte_cli viz astrocyte_example_wordcount
### Astrocyte workflow containers
The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the containers used by this workflow.
When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to
When the `astrocyte_cli` runs this workflow, it will pull the images in this section and save them to
`workflow/images/singularity/` for later use. In the workflow, the default configuration located in
`workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase,
toLines, and word count processes.
`workflow/configs/biohpc.config` defines how the Nextflow command will use the singularity executor for the uppercase,
toLines, cleanlines, and word count processes.
### Vizapp containers
......
......@@ -12,7 +12,7 @@
// Path to an input file, or a pattern for multiple inputs
// Note - $baseDir is the location of this workflow file main.nf
params.story = "$baseDir/../test_data/mobydick.txt"
params.story = "$baseDir/../test_data/*.txt"
// Parameters for test values, only used for demonstrating parameter types
params.test_int = 999
......
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