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Astrocyte
Workflows
Strand Lab
cellranger-count
Commits
e807faa9
Commit
e807faa9
authored
1 year ago
by
Felix Perez
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Update the documentation to include the new process.
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README.md
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README.md
docs/index.md
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docs/index.md
workflow/main.nf
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workflow/main.nf
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README.md
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e807faa9
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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.
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@@ -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
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docs/index.md
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@@ -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.
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@@ -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`
run
s
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
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workflow/main.nf
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@@ -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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