diff --git a/README.md b/README.md
index 949696a..5a258ed 100644
--- a/README.md
+++ b/README.md
@@ -54,13 +54,14 @@ graph LR
nextflow[Nextflow workflow]
- script & config --- viash_build --> docker_image & executable
+ component --- viash_build --> docker_image & executable
docker_image -.-> executable & nextflow
viash_build --> nextflow
nextflow --dependency--> nextflow
subgraph compute [Compute environment]
+ direction LR
local[Local execution]
awsbatch[AWS Batch]
googlebatch[Google Cloud Batch]
@@ -149,14 +150,14 @@ Output
[33mNextflow 24.04.3 is available - Please consider updating your version to it(B[m
N E X T F L O W ~ version 23.10.0
Pulling viash-io/viash_project_template ...
- Already-up-to-date
- Launching `https://github.com/viash-io/viash_project_template` [kickass_wescoff] DSL2 - revision: 5971837633 [build/main]
- [5c/8aaf68] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file2)
- [73/4b02d0] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file1)
- [1d/68933b] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file2)
- [5f/3cf8f1] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file1)
- [88/61f733] Submitted process > workflow:run_wf:combine_columns:processWf:combine_columns_process (combined)
- [97/67bc9f] Submitted process > workflow:publishStatesSimpleWf:publishStatesProc (combined)
+ Fast-forward
+ Launching `https://github.com/viash-io/viash_project_template` [high_booth] DSL2 - revision: 850d7a9a0b [build/main]
+ [d6/a1c458] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file2)
+ [8d/2c2769] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file1)
+ [33/99ab7b] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file2)
+ [d3/0558f7] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file1)
+ [bf/17413a] Submitted process > workflow:run_wf:combine_columns:processWf:combine_columns_process (combined)
+ [41/e8de88] Submitted process > workflow:publishStatesSimpleWf:publishStatesProc (combined)
@@ -205,6 +206,11 @@ Your new repository should contain the following files:
tree my_first_pipeline
```
+
+
+Output
+
+
.
├── CHANGELOG.md
├── LICENSE.md
@@ -326,6 +332,12 @@ tree my_first_pipeline
│ └── _viash_par
│ └── input_1
│ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/a2/364f5e24ac876c1c623e5108715c25/file1.remove_comments.output.tsv
+ ├── 33
+ │ └── 99ab7b871657561e53852ceffb2c3b
+ │ ├── file2.take_column.output.tsv
+ │ └── _viash_par
+ │ └── input_1
+ │ └── file2.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/d6/a1c45853eb77de60f7e418335572f7/file2.remove_comments.output.tsv
├── 34
│ └── 01b46f7b0e2e645ab666e5018eabae
│ ├── file2.take_column.output
@@ -344,6 +356,18 @@ tree my_first_pipeline
│ └── _viash_par
│ └── input_1
│ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/51/c6c6f3fdde45320e405d179f99d312/file1.remove_comments.output.tsv
+ ├── 3b
+ │ └── 03eccd1f1b72cc9573c75517768598
+ │ ├── combined.workflow.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/df/b8f21005023ec59164adf1b73c16f5/combined.combine_columns.output.tsv
+ │ ├── combined.workflow.state.yaml
+ │ └── _inputfile1
+ │ └── combined.combine_columns.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/df/b8f21005023ec59164adf1b73c16f5/combined.combine_columns.output.tsv
+ ├── 41
+ │ └── e8de8893710a2ceb0cd054eb575e85
+ │ ├── combined.workflow.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/bf/17413a5e9d5d7ed0263107ebcdd35c/combined.combine_columns.output.tsv
+ │ ├── combined.workflow.state.yaml
+ │ └── _inputfile1
+ │ └── combined.combine_columns.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/bf/17413a5e9d5d7ed0263107ebcdd35c/combined.combine_columns.output.tsv
├── 42
│ └── fc43ba6329aefa58093c2398bdad50
│ ├── combined.combine_columns.output
@@ -441,6 +465,11 @@ tree my_first_pipeline
│ └── input_1
│ └── file2.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/65/74f3824fa5c47fe39f4a7afa513ba3/file2.remove_comments.output.tsv
├── 6e
+ │ ├── 23e430564b01e0aded3ca6983ac873
+ │ │ ├── file2.remove_comments.output.tsv
+ │ │ └── _viash_par
+ │ │ └── input_1
+ │ │ └── file2.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file2.tsv
│ └── 6e14906d52ce474625898954ecdc23
│ ├── file2.take_column.output
│ └── _viash_par
@@ -459,6 +488,11 @@ tree my_first_pipeline
│ └── _inputfile1
│ └── combined.combine_columns.output -> /home/rcannood/workspace/viash-io/viash_project_template/work/4f/99d95392847652f65a764f0001159d/combined.combine_columns.output
├── 7d
+ │ ├── 7c9e5fa10e97e37a112d9e7934a5cf
+ │ │ ├── file2.take_column.output.tsv
+ │ │ └── _viash_par
+ │ │ └── input_1
+ │ │ └── file2.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/6e/23e430564b01e0aded3ca6983ac873/file2.remove_comments.output.tsv
│ └── aa34e2647eacc36dd144b6a643283f
│ ├── file2.remove_comments.output.tsv
│ └── _viash_par
@@ -496,6 +530,12 @@ tree my_first_pipeline
│ └── _viash_par
│ └── input_1
│ └── file2.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/bf/ab6cbd0018d747facdfd11a71a2c25/file2.remove_comments.output.tsv
+ ├── 8d
+ │ └── 2c2769f8c6eeaf83b65fbd3ae8b745
+ │ ├── file1.remove_comments.output.tsv
+ │ └── _viash_par
+ │ └── input_1
+ │ └── file1.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file1.tsv
├── 8f
│ └── 850c4d4b5974c7f0cae9c5168b2ae8
│ ├── file2.remove_comments.output.tsv
@@ -503,11 +543,22 @@ tree my_first_pipeline
│ └── input_1
│ └── file2.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file2.tsv
├── 91
- │ └── 4476a4387a1901b58422821cdb8fa7
- │ ├── file1.take_column.output
+ │ ├── 4476a4387a1901b58422821cdb8fa7
+ │ │ ├── file1.take_column.output
+ │ │ └── _viash_par
+ │ │ └── input_1
+ │ │ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/c2/de1bc7b847fe9c8633b88062cb9340/file1.remove_comments.output.tsv
+ │ └── 8c0ac0adc5db34536a78bdd0faf6fe
+ │ ├── file1.take_column.output.tsv
│ └── _viash_par
│ └── input_1
- │ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/c2/de1bc7b847fe9c8633b88062cb9340/file1.remove_comments.output.tsv
+ │ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/93/914f3c979e5d377f715114f888b288/file1.remove_comments.output.tsv
+ ├── 93
+ │ └── 914f3c979e5d377f715114f888b288
+ │ ├── file1.remove_comments.output.tsv
+ │ └── _viash_par
+ │ └── input_1
+ │ └── file1.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file1.tsv
├── 97
│ ├── 67bc9ff22c2f1fadc730d142de61bf
│ │ ├── combined.workflow.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/88/61f733186d443467b3efe1cd3b883a/combined.combine_columns.output.tsv
@@ -615,6 +666,13 @@ tree my_first_pipeline
│ └── input_2
│ └── file2.take_column.output -> /home/rcannood/workspace/viash-io/viash_project_template/work/48/8b8abb853b5655faca3e83b6cb87f4/file2.take_column.output
├── bf
+ │ ├── 17413a5e9d5d7ed0263107ebcdd35c
+ │ │ ├── combined.combine_columns.output.tsv
+ │ │ └── _viash_par
+ │ │ ├── input_1
+ │ │ │ └── file1.take_column.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/d3/0558f7d20cf213bddb41ff95087b21/file1.take_column.output.tsv
+ │ │ └── input_2
+ │ │ └── file2.take_column.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/33/99ab7b871657561e53852ceffb2c3b/file2.take_column.output.tsv
│ └── ab6cbd0018d747facdfd11a71a2c25
│ ├── file2.remove_comments.output.tsv
│ └── _viash_par
@@ -629,12 +687,24 @@ tree my_first_pipeline
├── c7
│ └── 7afec45f9f4b9db690a4cba6a00670
│ └── run.remove_comments.output.tsv
+ ├── d3
+ │ └── 0558f7d20cf213bddb41ff95087b21
+ │ ├── file1.take_column.output.tsv
+ │ └── _viash_par
+ │ └── input_1
+ │ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/8d/2c2769f8c6eeaf83b65fbd3ae8b745/file1.remove_comments.output.tsv
├── d4
│ └── 84823059b693efb2cc0eee9cbb7e3f
│ ├── file1.take_column.output
│ └── _viash_par
│ └── input_1
│ └── file1.remove_comments.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/da/fa0bfc9ac6fdd94a3d3c3d1a501e2d/file1.remove_comments.output.tsv
+ ├── d6
+ │ └── a1c45853eb77de60f7e418335572f7
+ │ ├── file2.remove_comments.output.tsv
+ │ └── _viash_par
+ │ └── input_1
+ │ └── file2.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file2.tsv
├── d7
│ └── 49029eb5446a27efc5479b06db24e2
│ ├── combined.workflow.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/a7/1be5d7138644b119c619b6ac5c29ff/combined.combine_columns.output
@@ -654,6 +724,14 @@ tree my_first_pipeline
│ └── _viash_par
│ └── input_1
│ └── file1.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file1.tsv
+ ├── df
+ │ └── b8f21005023ec59164adf1b73c16f5
+ │ ├── combined.combine_columns.output.tsv
+ │ └── _viash_par
+ │ ├── input_1
+ │ │ └── file1.take_column.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/91/8c0ac0adc5db34536a78bdd0faf6fe/file1.take_column.output.tsv
+ │ └── input_2
+ │ └── file2.take_column.output.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/work/7d/7c9e5fa10e97e37a112d9e7934a5cf/file2.take_column.output.tsv
├── e6
│ └── 35d4d3da9b59d4067d39160a4bfc29
│ ├── file1.remove_comments.output.tsv
@@ -687,7 +765,9 @@ tree my_first_pipeline
└── input_1
└── file1.tsv -> /home/rcannood/workspace/viash-io/viash_project_template/resources_test/file1.tsv
- 293 directories, 188 files
+ 337 directories, 216 files
+
+
### Step 2: Build the Viash components
@@ -703,13 +783,13 @@ viash ns build --setup cachedbuild --parallel
Output
- Exporting workflow (template) =nextflow=> target/nextflow/template/workflow
- Exporting take_column (template) =nextflow=> target/nextflow/template/take_column
- Exporting combine_columns (template) =executable=> target/executable/template/combine_columns
Exporting take_column (template) =executable=> target/executable/template/take_column
- Exporting remove_comments (template) =nextflow=> target/nextflow/template/remove_comments
+ Exporting take_column (template) =nextflow=> target/nextflow/template/take_column
Exporting combine_columns (template) =nextflow=> target/nextflow/template/combine_columns
Exporting remove_comments (template) =executable=> target/executable/template/remove_comments
+ Exporting remove_comments (template) =nextflow=> target/nextflow/template/remove_comments
+ Exporting workflow (template) =nextflow=> target/nextflow/template/workflow
+ Exporting combine_columns (template) =executable=> target/executable/template/combine_columns
[notice] Building container 'ghcr.io/viash-io/project_template/template/take_column:dev' with Dockerfile
[notice] Building container 'ghcr.io/viash-io/project_template/template/combine_columns:dev' with Dockerfile
[notice] Building container 'ghcr.io/viash-io/project_template/template/remove_comments:dev' with Dockerfile
@@ -779,13 +859,13 @@ Output
[33mNextflow 24.04.3 is available - Please consider updating your version to it(B[m
N E X T F L O W ~ version 23.10.0
- Launching `target/nextflow/template/workflow/main.nf` [modest_noyce] DSL2 - revision: 43ac230bc0
- [93/914f3c] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file1)
- [6e/23e430] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file2)
- [7d/7c9e5f] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file2)
- [91/8c0ac0] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file1)
- [df/b8f210] Submitted process > workflow:run_wf:combine_columns:processWf:combine_columns_process (combined)
- [3b/03eccd] Submitted process > workflow:publishStatesSimpleWf:publishStatesProc (combined)
+ Launching `target/nextflow/template/workflow/main.nf` [high_hilbert] DSL2 - revision: f68ea52db6
+ [7e/d31ed4] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file1)
+ [0a/90dd2e] Submitted process > workflow:run_wf:remove_comments:processWf:remove_comments_process (file2)
+ [72/fb17ac] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file2)
+ [44/0f47bd] Submitted process > workflow:run_wf:take_column:processWf:take_column_process (file1)
+ [88/8ff83f] Submitted process > workflow:run_wf:combine_columns:processWf:combine_columns_process (combined)
+ [15/3aaf04] Submitted process > workflow:publishStatesSimpleWf:publishStatesProc (combined)
@@ -802,10 +882,10 @@ cat output/combined.workflow.output.tsv
Output
- "1" 0.11 0.111
- "2" 0.23 0.222
- "3" 0.35 0.333
- "4" 0.47 0.444
+ "1" 0.111 0.11
+ "2" 0.222 0.23
+ "3" 0.333 0.35
+ "4" 0.444 0.47
diff --git a/README.qmd b/README.qmd
index e0c8da4..de7b488 100644
--- a/README.qmd
+++ b/README.qmd
@@ -45,13 +45,14 @@ graph LR
nextflow[Nextflow workflow]
- script & config --- viash_build --> docker_image & executable
+ component --- viash_build --> executable & docker_image & nextflow
docker_image -.-> executable & nextflow
- viash_build --> nextflow
+
nextflow --dependency--> nextflow
subgraph compute [Compute environment]
+ direction LR
local[Local execution]
awsbatch[AWS Batch]
googlebatch[Google Cloud Batch]
@@ -176,10 +177,15 @@ Your new repository should contain the following files:
tree my_first_pipeline
```
+
+Output
+
```{bash echo=FALSE}
tree .
```
+
+
### Step 2: Build the Viash components
With Viash you can turn the components in `src/` into Dockerized Nextflow modules by running: