Merge pull request #133 from skrakau/fix_input

Fix processing of input parameter
nf-core · Nov 19, 2020 · e26244b · e26244b
2 parents 98d5aa0 + e07a04e
commit e26244b
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Showing 4 changed files with 14 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.2.0dev - [date]
 
+### `Fixed`
+
+- [#133](https://github.com/nf-core/mag/pull/133) - Fixed processing of `--input` parameter
+
 ## v1.1.1 - 2019/11/10
 
 ### `Added`

diff --git a/main.nf b/main.nf
@@ -280,8 +280,8 @@ if(params.manifest){
     }
  } else {
     Channel
-        .fromFilePairs(params.reads, size: params.single_end ? 1 : 2)
-        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
+        .fromFilePairs(params.input, size: params.single_end ? 1 : 2)
+        .ifEmpty { exit 1, "Cannot find any reads matching: ${params.input}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
         .into { read_files_fastqc; read_files_fastp }
     files_long_raw = Channel.from()
 }

diff --git a/nextflow.config b/nextflow.config
@@ -66,6 +66,9 @@ params {
   spadeshybrid_fix_cpus = false
   metabat_rng_seed = 1
 
+  // For testing
+  input_paths = false
+
   // Boilerplate options
   name = false
   multiqc_config = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -22,6 +22,11 @@
                     "description": "Manifest file, required for hybrid assembly with metaSPAdes. Alternative to `--input`.",
                     "help_text": "Has 4 headerless columns (tab separated): Sample_Id, Long_Reads, Short_Reads_1, Short_Reads_2\n"
                 },
+                "input_paths": {
+                    "type": "string",
+                    "description": "Paths to input FastQ files for tests.",
+                    "hidden": true
+                },
                 "single_end": {
                     "type": "boolean",
                     "description": "Specifies that the input is single-end reads.",