Make --outdir mandatory nf-core/tools#1415

drpatelh · Feb 18, 2022 · 70d0c0b · 70d0c0b
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Showing 14 changed files with 36 additions and 26 deletions.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/vira
     - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/viralrecon/tree/master/.github/CONTRIBUTING.md)
     - [ ] If necessary, also make a PR on the nf-core/viralrecon _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
 
   parameters:
     name: Test workflow parameters
@@ -74,7 +74,7 @@ jobs:
 
       - name: Run pipeline with various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
 
   test_sispa:
     name: Test SISPA workflow
@@ -96,7 +96,7 @@ jobs:
 
       - name: Run pipeline with minimal SISPA data and various options
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }} --outdir ./results
 
   test_nanopore:
     name: Test Nanopore workflow
@@ -122,4 +122,4 @@ jobs:
 
       - name: Run pipeline with minimal Nanopore data and various options
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }} --outdir ./results
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * [[#281](https://github.com/nf-core/viralrecon/issues/281)] - Nanopore medaka processing fails with error if model name, not model file, provided
+* [nf-core/tools#1415](https://github.com/nf-core/tools/issues/1415) - Make `--outdir` a mandatory parameter
 
 ### Parameters
 

diff --git a/README.md b/README.md
@@ -87,7 +87,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/viralrecon -profile test,YOURPROFILE
+    nextflow run nf-core/viralrecon -profile test,YOURPROFILE --outdir <OUTDIR>
     ```
 
     Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -104,6 +104,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
         ```bash
         nextflow run nf-core/viralrecon \
             --input samplesheet.csv \
+            --outdir <OUTDIR>
             --platform illumina \
             --protocol metagenomic \
             --genome 'MN908947.3' \
@@ -115,6 +116,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
         ```bash
         nextflow run nf-core/viralrecon \
             --input samplesheet.csv \
+            --outdir <OUTDIR>
             --platform illumina \
             --protocol amplicon \
             --genome 'MN908947.3' \
@@ -129,6 +131,7 @@ A number of improvements were made to the pipeline recently, mainly with regard
         ```bash
         nextflow run nf-core/viralrecon \
             --input samplesheet.csv \
+            --outdir <OUTDIR>
             --platform nanopore \
             --genome 'MN908947.3' \
             --primer_set_version 3 \

diff --git a/conf/test.config b/conf/test.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/viralrecon -profile test,<docker/singularity>
+        nextflow run nf-core/viralrecon -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -32,7 +32,7 @@ params {
 
     // Variant calling options
     variant_caller = 'ivar'
-    
+
     // Assembly options
     assemblers     = 'spades,unicycler,minia'
     skip_plasmidid = true  // Skip this by default to bypass Github Actions disk quota errors

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/viralrecon -profile test_full,<docker/singularity>
+        nextflow run nf-core/viralrecon -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_full_nanopore.config b/conf/test_full_nanopore.config
@@ -2,10 +2,10 @@
 ========================================================================================
     Nextflow config file for running full-size tests
 ========================================================================================
-    Defines input files and everything required to run a full size pipeline test. 
-    
+    Defines input files and everything required to run a full size pipeline test.
+
     Use as follows:
-        nextflow run nf-core/viralrecon -profile test_full_nanopore,<docker/singularity>
+        nextflow run nf-core/viralrecon -profile test_full_nanopore,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -20,11 +20,11 @@ params {
     fastq_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/fastq_pass/'
     fast5_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/fast5_pass/'
     sequencing_summary = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/sequencing_summary.txt'
-    
+
     // Genome references
     genome             = 'MN908947.3'
     primer_set_version = 3
 
     // Other parameters
     artic_minion_medaka_model = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/r941_min_high_g360_model.hdf5'
-}
+}
diff --git a/conf/test_full_sispa.config b/conf/test_full_sispa.config
@@ -2,10 +2,10 @@
 ========================================================================================
     Nextflow config file for running full-size tests
 ========================================================================================
-    Defines input files and everything required to run a full size pipeline test. 
-    
+    Defines input files and everything required to run a full size pipeline test.
+
     Use as follows:
-        nextflow run nf-core/viralrecon -profile test_full_sispa,<docker/singularity>
+        nextflow run nf-core/viralrecon -profile test_full_sispa,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -33,4 +33,4 @@ process {
     withName: 'PLASMIDID' {
         errorStrategy = 'ignore'
     }
-}
+}
diff --git a/conf/test_nanopore.config b/conf/test_nanopore.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/viralrecon -profile test_nanopore,<docker/singularity>
+        nextflow run nf-core/viralrecon -profile test_nanopore,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_sispa.config b/conf/test_sispa.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/viralrecon -profile test_sispa,<docker/singularity>
+        nextflow run nf-core/viralrecon -profile test_sispa,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -30,7 +30,7 @@ params {
 
     // Variant calling options
     variant_caller = 'bcftools'
-    
+
     // Assembly options
     assemblers     = 'spades,unicycler,minia'
     skip_plasmidid = true  // Skip this by default to bypass Github Actions disk quota errors

diff --git a/docs/usage.md b/docs/usage.md
@@ -97,6 +97,7 @@ The command to run the pipeline would then be:
 ```console
 nextflow run nf-core/viralrecon \
     --input samplesheet.csv \
+    --outdir <OUTDIR> \
     --platform nanopore \
     --genome 'MN908947.3' \
     --primer_set_version 3 \
@@ -115,6 +116,7 @@ The command to run the pipeline would then be:
 ```console
 nextflow run nf-core/viralrecon \
     --input samplesheet.csv \
+    --outdir <OUTDIR> \
     --platform nanopore \
     --genome 'MN908947.3' \
     --primer_set_version 3 \
@@ -139,6 +141,7 @@ An example command using v3 ARTIC primers with "MN908947.3":
 ```console
 nextflow run nf-core/viralrecon \
     --input samplesheet.csv \
+    --outdir <OUTDIR> \
     --platform illumina \
     --protocol amplicon \
     --genome 'MN908947.3' \
@@ -157,6 +160,7 @@ An example command using SWIFT primers with "MN908947.3":
 ```console
 nextflow run nf-core/viralrecon \
     --input samplesheet.csv \
+    --outdir <OUTDIR> \
     --platform illumina \
     --protocol amplicon \
     --genome 'MN908947.3' \
@@ -173,7 +177,7 @@ nextflow run nf-core/viralrecon \
 The typical command for running the pipeline is as follows:
 
 ```console
-nextflow run nf-core/viralrecon --input samplesheet.csv --genome 'MN908947.3' -profile docker
+nextflow run nf-core/viralrecon --input samplesheet.csv --outdir <OUTDIR> --genome 'MN908947.3' -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -21,7 +21,7 @@ class WorkflowMain {
     // Print help to screen if required
     //
     public static String help(workflow, params, log) {
-        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome 'MN908947.3' -profile docker"
+        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --outdir <OUTDIR> --genome 'MN908947.3' -profile docker"
         def help_string = ''
         help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
         help_string += NfcoreSchema.paramsHelp(workflow, params, command)

diff --git a/nextflow.config b/nextflow.config
@@ -90,7 +90,7 @@ params {
     skip_assembly              = false
 
     // Boilerplate options
-    outdir                     = './results'
+    outdir                     = null
     tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,6 +10,9 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
+            "required": [
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -42,8 +45,7 @@
                 "outdir": {
                     "type": "string",
                     "format": "directory-path",
-                    "description": "The output directory where the results will be saved.",
-                    "default": "./results",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
                 "email": {