Merge branch 'dev' into ci-nf-test

Author: maxulysse

.nf-core.yml

@@ -4,6 +4,9 @@ lint:
     - .github/CONTRIBUTING.md
   files_exist:
     - .github/workflows/ci.yml
+  nextflow_config:
+    - config_defaults:
+        - params.fastq_screen_references
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -21,12 +21,17 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#53](https://github.com/nf-core/seqinspector/pull/53) Add FastQ-Screen database multiplexing and limit scope of nf-test in CI.
 - [#96](https://github.com/nf-core/seqinspector/pull/96) Added missing citations to citation tool
 - [#103](https://github.com/nf-core/seqinspector/pull/103) Configure full-tests
+- [#110](https://github.com/nf-core/seqinspector/pull/110) Update input schema to accept either tar file or directory as rundir, and fastq messages and patterns.
 
 ### `Fixed`
 
 - [#71](https://github.com/nf-core/seqinspector/pull/71) FASTQSCREEN does not fail when multiple reads are provided.
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
+- [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
+- [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
 
 ### `Dependencies`
 
+- [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28
+
 ### `Deprecated`

assets/schema_input.json

@@ -17,21 +17,31 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ files for read 1 must be provided and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+                "pattern": "\\.f(ast)?q\\.gz$",
+                "errorMessage": "FastQ files for read 2 are optional and must have extension '.fq.gz' or '.fastq.gz' if provided"
             },
             "rundir": {
-                "type": "string",
-                "format": "path",
-                "exists": true,
-                "errorMessage": "Run directory must be a path",
+                "oneOf": [
+                    {
+                        "type": "string",
+                        "format": "file-path",
+                        "exists": true,
+                        "pattern": "\\.tar\\.gz$"
+                    },
+                    {
+                        "type": "string",
+                        "format": "directory-path",
+                        "exists": true
+                    }
+                ],
+                "errorMessage": "Run directory must be a path or tar directory",
                 "meta": ["rundir"]
             },
             "tags": {

conf/modules.config

@@ -31,7 +31,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/seqfu_stats" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.sample_id}_$filename" }
         ]
     }
 

modules.json

@@ -28,7 +28,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
                     "seqfu/stats": {

modules/nf-core/multiqc/environment.yml

@@ -21,7 +21,7 @@ params {
     igenomes_ignore            = false
 
     // Fastqscreen options
-    fastq_screen_references    = './assets/example_fastq_screen_references.csv'
+    fastq_screen_references    = "${projectDir}/assets/example_fastq_screen_references.csv"
 
     // MultiQC options
     multiqc_config             = null

modules/nf-core/multiqc/main.nf

@@ -94,7 +94,7 @@
                 },
                 "fastq_screen_references": {
                     "type": "string",
-                    "default": "./assets/example_fastq_screen_references.csv",
+                    "default": "${projectDir}/assets/example_fastq_screen_references.csv",
                     "fa_icon": "fas fa-search",
                     "description": "A .csv of reference genomes to be mapped against by FastQ Screen"
                 }

modules/nf-core/multiqc/tests/main.nf.test.snap

@@ -1,11 +1,11 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf on MiSeq data"
+    name "Test Workflow main.nf on MiSeq data with single end reads"
     script "../main.nf"
     tag "seqinspector"
     tag "PIPELINE"
 
-    test("MiSeq data test") {
+    test("MiSeq data test (single end reads)") {
 
         when {
             config "./MiSeq.main.nf.test.config"