FEAT: untar input directory if needed. (#4)

* FEAT: untar input directory if needed.

* Fixes to untar component

* Fix workflow including untar

* Check for .tar and .tgz as well

* Remove debugging output from tar component

* Add target and testData folder to .gitignore

* Update to latest release candidate

* Add .nextflow and work to .gitignore

* Add runners to untar component

* Update workflow integration test

* Remove leftover view

---------

Co-authored-by: Toni Verbeiren <[email protected]>

.gitignore

@@ -0,0 +1,6 @@
+target
+testData
+
+# Nextflow related files
+.nextflow
+work

_viash.yaml

@@ -7,4 +7,4 @@ links:
   issue_tracker: https://github.com/viash-hub/demultiplex.vsh/issues
   repository: https://github.com/viash-hub/demultiplex.vsh
 
-viash_version: 0.9.0-RC2
+viash_version: 0.9.0-RC3

src/demultiplex/config.vsh.yaml

@@ -29,6 +29,8 @@ test_resources:
     entrypoint: test_wf
 
 dependencies:
+  - name: io/untar
+    repository: local
   - name: bcl_convert
     repository: bb
 

src/demultiplex/integration_tests.sh

@@ -1,3 +1,13 @@
+#!/usr/bin/env bash
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+viash ns build -q 'untar|demultiplex' --setup cb
+
 nextflow run . \
   -main-script src/demultiplex/test.nf \
   -profile docker,no_publish \

src/demultiplex/main.nf

@@ -4,7 +4,19 @@ workflow run_wf {
 
   main:
     output_ch = input_ch
-
+      // untar input if needed
+      | untar.run(
+        runIf: {id, state -> 
+          def inputStr = state.input.toString()
+          inputStr.endsWith(".tar.gz") || inputStr.endsWith(".tar") || inputStr.endsWith(".tgz") ? true : false
+        },
+        fromState: [
+          "input": "input",
+        ],
+        toState: { id, result, state ->
+          state + [ input: result.output ]
+        },
+      )
       // run bcl_convert
       | bcl_convert.run(
           fromState: { id, state ->

src/demultiplex/test.nf

@@ -3,13 +3,12 @@ nextflow.enable.dsl=2
 include { demultiplex } from params.rootDir + "/target/nextflow/demultiplex/main.nf"
 
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/testData")
-
   output_ch = Channel.fromList([
         [
-          sample_sheet: resources_test.resolve("bcl_convert_samplesheet.csv"),
-          input: resources_test.resolve("iseq-DI/"),
+          // sample_sheet: resources_test.resolve("bcl_convert_samplesheet.csv"),
+          // input: resources_test.resolve("iseq-DI/"),
+          sample_sheet: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/SampleSheet.csv",
+          input: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
           publish_dir: "output_dir/",
         ]
       ])

src/io/untar/config.vsh.yaml

@@ -33,4 +33,8 @@ test_resources:
     path: test.sh
 engines:
   - type: docker
-    image: debian:stable-slim
+    image: debian:stable-slim
+
+runners:
+  - type: executable
+  - type: nextflow