From 2bda37388ca71ec07c9d851140e41480782f30f2 Mon Sep 17 00:00:00 2001
From: Sarah Griffiths <sarah.griffiths@nanoporetech.com>
Date: Tue, 5 Sep 2023 08:57:28 +0000
Subject: [PATCH] Update fastqingress.nf

---
 lib/fastqingress.nf | 14 +++++++-------
 nextflow.config     |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/fastqingress.nf b/lib/fastqingress.nf
index 42e6f5c..a353996 100644
--- a/lib/fastqingress.nf
+++ b/lib/fastqingress.nf
@@ -311,7 +311,13 @@ def get_valid_inputs(Map margs){
                 [create_metamap([alias: margs["sample"] ?: input.baseName]), input])
         } else {
             // deal with the second case (sub-directories with fastq data) --> first
-            // check whether we actually found sub-directories
+            // check whether we actually found sub-directories (and remove
+            // sub-directories called 'unclassified' unless otherwise specified)
+            if (!margs.analyse_unclassified) {
+                sub_dirs_with_fastq_files = sub_dirs_with_fastq_files.findAll {
+                    it.baseName != "unclassified"
+                }
+            }
             if (!sub_dirs_with_fastq_files) {
                 error "Input directory '$input' must contain either FASTQ files " +
                     "or sub-directories containing FASTQ files."
@@ -325,12 +331,6 @@ def get_valid_inputs(Map margs){
                 error "Input directory '$input' cannot contain more " +
                     "than one level of sub-directories with FASTQ files."
             }
-            // remove directories called 'unclassified' unless otherwise specified
-            if (!margs.analyse_unclassified) {
-                sub_dirs_with_fastq_files = sub_dirs_with_fastq_files.findAll {
-                    it.baseName != "unclassified"
-                }
-            }
             // filter based on sample sheet in case one was provided
             if (margs.sample_sheet) {
                 // get channel of entries in the sample sheet
diff --git a/nextflow.config b/nextflow.config
index 746fd75..2899d08 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -104,7 +104,7 @@ params {
       ]
     agent = null
     container_sha = "sha203915eb4b4dd444cb2e845d0b9f7814e26b7b5c"
-    common_sha = "sha5fc720674a26bc63a6f31ed186344209175b54b1"
+    common_sha = "sha0a6dc21fac17291f4acb2e0f67bcdec7bf63e6b7"
     }
 }