Fix YAML validation errors

test-datasets

@@ -1 +1 @@
-Subproject commit aae85a5c9c72238959108212481ce83bae569709
+Subproject commit e5fef88994b8d34c7bf4b07116e5f7a330d2ee3b

tools/bowtie2/meta.yml

@@ -28,10 +28,10 @@ output:
         - report:
             type: file
             description: mapping statistics report
-            pattern: *bowtie2_stats.txt
+            pattern: "*bowtie2_stats.txt"
         - alignment:
             type: file
             description: alignment file in BAM format
-            pattern: *bowtie2.bam
+            pattern: "*bowtie2.bam"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"

tools/bwa/index/meta.yml

@@ -14,12 +14,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - index:
             type: file
             description: bwa indexes file
-            pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
+            pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
 authors:
-    - @maxulysse
+    - "@maxulysse"

tools/bwa/mem/meta.yml

@@ -19,11 +19,11 @@ input:
         - reads:
             type: file
             description: Input fastq file
-            pattern: *.{fastq,fq}
+            pattern: "*.{fastq,fq}"
         - index:
             type: file
             description: bwa indexes file
-            pattern: *.{amb,ann,bwt,pac,sa}
+            pattern: "*.{amb,ann,bwt,pac,sa}"
         - prefix:
             type: val
             description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
@@ -32,11 +32,11 @@ output:
         - bam:
             type: file
             description: Output bam file
-            pattern: *.bam
+            pattern: "*.bam"
         - bamindex:
             type: file
             description: Output bam index file
-            pattern: *.bai
+            pattern: "*.bai"
 
 authors:
-    - @jeremy1805
+    - "@jeremy1805"

tools/cutadapt/meta.yml

@@ -33,4 +33,4 @@ output:
             type: file
             description: trimmed FastQ file, or pair of files
 authors:
-    - @piotr-faba-ardigen
+    - "@piotr-faba-ardigen"

tools/fastq_screen/meta.yml

@@ -25,7 +25,7 @@ output:
         - report:
             type: file
             description: FastQ Screen report
-            pattern: *_screen.{txt,html,png}
+            pattern: "*_screen.{txt,html,png}"
-            optional_pattern: *_screen.bisulfite_orientation.png
+            optional_pattern: "*_screen.bisulfite_orientation.png"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"

tools/fastqc/meta.yml

@@ -27,8 +27,7 @@ output:
         - report:
             type: file
             description: FastQC report
-            pattern: *_fastqc.{zip,html}
+            pattern: "*_fastqc.{zip,html}"
 authors:
-    -
+    - "@ewels"
-        - @ewels
+    - "@FelixKrueger"
-        - @FelixKrueger

tools/gatk/dict/meta.yml

@@ -14,12 +14,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - dict:
             type: file
             description: gatk dictionary file
-            pattern: *.{fasta,fa}.{dict}
+            pattern: "*.{fasta,fa}.{dict}"
 authors:
-    - @maxulysse
+    - "@maxulysse"

tools/hisat2/meta.yml

@@ -28,10 +28,10 @@ output:
         - report:
             type: file
             description: mapping statistics report
-            pattern: *hisat2_stats.txt
+            pattern: "*hisat2_stats.txt"
         - alignment:
             type: file
             description: alignment file in BAM format
-            pattern: *hisat2.bam
+            pattern: "*hisat2.bam"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"

tools/htslib/tabix/meta.yml

@@ -15,12 +15,12 @@ input:
         - input:
             type: file
             description: Input vcf.gz file
-            pattern: *.{vcf.gz}
+            pattern: "*.{vcf.gz}"
 output:
     -
         - index:
             type: file
             description: tabix index file
-            pattern: *.{vcf.gz.tbi}
+            pattern: "*.{vcf.gz.tbi}"
 authors:
-    - @maxulysse
+    - "@maxulysse"

tools/multiqc/meta.yml

@@ -21,6 +21,6 @@ output:
         - multiqc_report:
             type: file
             description: MultiQC report
-            pattern: *multiqc*.html
+            pattern: "*multiqc*.html"
 authors:
-    - @FelixKrueger
+    - "@FelixKrueger"

tools/samtools/faidx/meta.yml

@@ -16,12 +16,12 @@ input:
         - input:
             type: file
             description: Input fasta file
-            pattern: *.{fasta,fa}
+            pattern: "*.{fasta,fa}"
 output:
     -
         - faidx:
             type: file
             description: samtools index fasta file
-            pattern: *.fasta.fai
+            pattern: "*.fasta.fai"
 authors:
-    - @maxulysse
+    - "@maxulysse"

tools/samtools/index/meta.yml

@@ -16,12 +16,12 @@ input:
         - input:
             type: file
             description: Input BAM or CRAM file
-            pattern: *.{bam,cram}
+            pattern: "*.{bam,cram}"
 output:
     -
         - index:
             type: file
             description: BAM or CRAM index file
-            pattern: *.{bai}
+            pattern: "*.{bai}"
 authors:
-    - @ewels
+    - "@ewels"

tools/samtools/sort/meta.yml

@@ -16,12 +16,12 @@ input:
         - input:
             type: file
             description: Input BAM or CRAM file
-            pattern: *.{bam,cram}
+            pattern: "*.{bam,cram}"
 output:
     -
         - sorted_file:
             type: file
             description: Sorted BAM or CRAM file
-            pattern: *.{bam,cram}
+            pattern: "*.{bam,cram}"
 authors:
-    - @ewels
+    - "@ewels"

tools/shovill/meta.yml

@@ -27,4 +27,4 @@ output:
             description: fasta file
             pattern: ${sample_id}.fasta
 authors:
-    - @annacprice
+    - "@annacprice"

tools/tcoffee/meta.yml

@@ -16,13 +16,13 @@ input:
         - fasta:
             type: path
             description: Input fasta file
-            pattern: *.{fasta,fa,tfa}
+            pattern: "*.{fasta,fa,tfa}"
 output:
     -
         - alignment:
             type: file
             description: tcoffee alignment file
-            pattern: *.aln
+            pattern: "*.aln"
 
 authors:
-    - @JoseEspinosa
+    - "@JoseEspinosa"

tools/trim_galore/meta.yml

@@ -28,14 +28,13 @@ output:
         - trimmed_fastq:
             type: file
             description: Trimmed FastQ files
-            pattern: *fq.gz
+            pattern: "*fq.gz"
     -
         - report:
             type: file
             description: Trim Galore! trimming report
-            pattern: *trimming_report.txt
+            pattern: "*trimming_report.txt"
 
 authors:
-    -
+    - "@ewels"
-        - @ewels
+    - "@FelixKrueger"
-        - @FelixKrueger

tools/umi_tools/umi_tools.yml

@@ -31,15 +31,15 @@ processes:
             - dedupBam:
                 type: tuple
                 description: A tuple of samples id and output bam file
-                pattern: [sample_id, *SAMPLE_ID.dedup.bam]
+                pattern: [sample_id, "*SAMPLE_ID.dedup.bam"]
             - dedupBam:
                 type: tuple
                 description: A tuple of samples id and output bai file
-                pattern: [sample_id, *SAMPLE_ID.dedup.bam.bai]
+                pattern: [sample_id, "*SAMPLE_ID.dedup.bam.bai"]
             - report:
                 type: file
                 description: Log file for the umi_tools operation
-                pattern: *SAMPLE_ID.dedup.log
+                pattern: "*SAMPLE_ID.dedup.log"
 authors:
-    - @candiceh08
+    - "@candiceh08"
-    - @chris-cheshire
+    - "@chris-cheshire"