Merge pull request #158 from Daniel-VM/concatenate_fasqs

Added module to concatenate/merge fastq files
nf-core · Oct 25, 2024 · efe6309 · efe6309
2 parents 064996b + 10a7df8
commit efe6309
Show file tree

Hide file tree

Showing 12 changed files with 792 additions and 14 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#176](https://github.com/nf-core/bacass/pull/176) Update nf-core/bacass to nf-core-tools v3.0.2 `TEMPLATE`.
 - [#166](https://github.com/nf-core/bacass/pull/166) Added FastQC after-trimming section to MultiQC report.
+- [#158](https://github.com/nf-core/bacass/pull/158) Support automatic concatenation of FastQ files for the same sample.
 
 ### `Fixed`
 

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -10,7 +10,7 @@
             "ID": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "unique": true,
+                "unique": false,
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },

diff --git a/conf/test.config b/conf/test.config
@@ -23,7 +23,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'
+    input = params.pipelines_testdata_base_path + 'bacass/bacass_short_reseq.tsv'
 
     // some extra args to speed tests up
     prokka_args     = " --fast"

diff --git a/modules.json b/modules.json
@@ -20,6 +20,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "cat/fastq": {
+                        "branch": "master",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["modules"]
+                    },
                     "dragonflye": {
                         "branch": "master",
                         "git_sha": "a3ae45e99f68e513b0feb8d5f27e2fdd0d0f083d",

diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml