Merge pull request #3 from Eco-Flow/gitpod_edits

Gitpod_edits
Eco-Flow · Apr 5, 2024 · 126c3a5 · 126c3a5
2 parents 05ef2b5 + e19ae21
commit 126c3a5
Show file tree

Hide file tree

Showing 9 changed files with 61 additions and 6 deletions.
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -1,3 +1,5 @@
+image: nfcore/gitpod:latest
+
 # List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/
 tasks:    
   - name: Download Nextflow Tutorial
@@ -10,6 +12,8 @@ tasks:
       nextflow info
       unset JAVA_TOOL_OPTIONS
       echo 'Starting workspace !'
+      sudo apt-get update
+      sudo apt-get install -y screen
 # List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/
 ports:
   - port: 8000
diff --git a/README.md b/README.md
@@ -230,6 +230,12 @@ nextflow run main.nf -profile apptainer,local -resume \
 nextflow run main.nf -profile docker,aws_batch -resume --input data/input_manual.csv --database "s3://pollen-metabarcoding-test-data/data/viridiplantae_all_2014.sintax.fa" --FW_primer "ATGCGATACTTGGTGTGAAT" --RV_primer "GCATATCAATAAGCGGAGGA" --custom_config /path/to/custom/config
 ```
 
+* Running on Gitpod:
+If you wish to run on Gitpod, please be aware that the usearch (sintax_summary) module will fail, as Gitpod doesn't allow 32bit programs.
+```
+nextflow run main.nf -profile docker,test_small -resume --gitpod
+```
+
 ## Test Data 
 The data used to test this pipeline via the [ENA ID: PRJEB26439](http://www.ebi.ac.uk/ena/data/view/PRJEB26439).
 There are two test profiles using this data:

diff --git a/main.nf b/main.nf
@@ -91,8 +91,10 @@ workflow {
   VSEARCH_SINTAX(ch_sintax.fa, ch_sintax.db)
   ch_versions = ch_versions.mix(VSEARCH_SINTAX.out.versions.first())
 
+  if (params.gitpod == null){
   USEARCH_SINTAX_SUMMARY(VSEARCH_SINTAX.out.tsv)
   ch_versions = ch_versions.mix(USEARCH_SINTAX_SUMMARY.out.versions.first())
+  }
 
   //Sometimes sintax produces different row lengths, only need first 2
   CUTTING(VSEARCH_SINTAX.out.tsv) | R_PROCESSING

diff --git a/nextflow.config b/nextflow.config
@@ -57,6 +57,8 @@ params {
   sintax_cutoff              = null
   sintax_strand              = null
   seed                       = 1312
+  //gitpod
+  gitpod                     = null
   //defaults used by Eco-Flow when testing, overwrite on command-line with your own resources
   awsqueue                   = 'HUNDRED_QUEUE'
   awsregion                  = 'us-east-1'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -191,6 +191,10 @@
         "forks": {
           "type": "number",
           "description": "Maximum number of each process that will be run in parallel."
+        },
+        "gitpod": {
+          "type": "boolean",
+          "description": "Skips usearch process, which does not run on gitpod (32bit)"
         }
       }
     },

diff --git a/tests/modules/local/r_processing.nf.test.snap b/tests/modules/local/r_processing.nf.test.snap
@@ -2,12 +2,12 @@
     "r_processing": {
         "content": [
             "ERR2537816.classified.tsv:md5,d7536874f239e304cca7667dc1ffde4d",
-            "summary.tsv:md5,4a575d1bc4bfb5f79cf160ae793e9c30"
+            "summary.tsv:md5,cdd728c2daee0aa13fcee439ff3460c2"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-27T13:36:37.712309"
+        "timestamp": "2024-04-04T11:11:20.884715539"
     }
 }
diff --git a/tests/modules/nf-core/cutadapt/main.nf.test.snap b/tests/modules/nf-core/cutadapt/main.nf.test.snap
@@ -1,13 +1,13 @@
 {
     "cutadapt_fastqs": {
         "content": [
-            "ERR2537816_1.trim.fastq.gz:md5,f9cb0dd1a4e2c3c871358d4d8dc7e490",
-            "ERR2537816_2.trim.fastq.gz:md5,c8333cd8e2f72a52122edf20ed159421"
+            "ERR2537816_1.trim.fastq.gz:md5,e9c82243f237a047eb2e095ed08da2f8",
+            "ERR2537816_2.trim.fastq.gz:md5,757f99993765c836965d6633bfbb5c97"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-27T13:54:45.929629"
+        "timestamp": "2024-04-05T11:14:03.65794141"
     }
 }
diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf.test b/tests/modules/nf-core/vsearch/sintax/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
               assert tsv[0].size() == 2
               assert tsv[0][0].size() == 2
             }
-
+            assert snapshot(process.out).match()
         }
 
     }

diff --git a/tests/modules/nf-core/vsearch/sintax/main.nf.test.snap b/tests/modules/nf-core/vsearch/sintax/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "ERR2537816",
+                            "single_end": false
+                        },
+                        "ERR2537816.tsv:md5,84351a56e4ddf56df7403c9ffefa0f1b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6584e256329124c6abe9e76715edfe92"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "ERR2537816",
+                            "single_end": false
+                        },
+                        "ERR2537816.tsv:md5,84351a56e4ddf56df7403c9ffefa0f1b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6584e256329124c6abe9e76715edfe92"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-04T12:52:09.921597141"
+    }
+}