Update modules

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#214](https://github.com/nf-core/demultiplex/pull/214) Updated method for removing adapters from samplesheet, added custom AdapterRemover function.
 - [#210](https://github.com/nf-core/demultiplex/pull/212) Update bcl2fastq and bcl_demultiplex.
 - [#216](https://github.com/nf-core/demultiplex/pull/216) List fastq reports for R1 and R2 separately in multiqc report.
+- [#217](https://github.com/nf-core/demultiplex/pull/217) Update all nf-core modules and tests.
 
 ## 1.4.1 - 2024-02-27
 

assets/multiqc_config.yml

@@ -22,6 +22,9 @@ sp:
 
 top_modules:
   - "bcl2fastq"
+  - "bclconvert"
+  - "bases2fastq"
+  - "mkfastq"
   - "checkqc"
   - "fastqc":
       name: "FastQC / Falco (Unpaired data)"

conf/modules.config

@@ -94,7 +94,7 @@ process {
             [
                 path: { "${params.outdir}/${meta.id}/" },
                 mode: params.publish_dir_mode,
-                pattern: "output/Samples/*/*.{json,fastq.gz}",
+                pattern: "output/Samples/**/*.{json,fastq.gz}",
                 saveAs: { filename -> filename.minus("output/") }
             ],
             [

modules.json

@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bases2fastq": {
                         "branch": "master",
-                        "git_sha": "c2342b45bbfc5d6fe19cc4154b38fa57177c67dd",
+                        "git_sha": "c651992bf8425fecefe14085ff486f42172cba77",
                         "installed_by": ["modules"]
                     },
                     "bcl2fastq": {
@@ -17,7 +17,7 @@
                     },
                     "bclconvert": {
                         "branch": "master",
-                        "git_sha": "54cd970e633efbd6adab9fc5610dd280e50ab32c",
+                        "git_sha": "1eed98385a32f1cd2bc38784450e200113b395e6",
                         "installed_by": ["bcl_demultiplex"]
                     },
                     "cellranger/mkfastq": {
@@ -32,7 +32,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
+                        "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
                         "installed_by": ["modules"]
                     },
                     "falco": {
@@ -42,27 +42,27 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
                     "fqtk": {
                         "branch": "master",
-                        "git_sha": "97a796133cd9644ba3dd83d3c0fd09a9a63b1a84",
+                        "git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
                         "installed_by": ["modules"]
                     },
                     "md5sum": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "1164836d4d3922ab937865b17086485f0f472748",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "sgdemux": {
@@ -72,7 +72,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     }
                 }