From 47d55001fad1b74a3603725cdacbc29655a7cb9a Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sat, 11 Jul 2020 13:54:12 +0200 Subject: [PATCH] Fix YAML validation errors --- test-datasets | 2 +- tools/bowtie2/meta.yml | 6 +++--- tools/bwa/index/meta.yml | 6 +++--- tools/bwa/mem/meta.yml | 10 +++++----- tools/cutadapt/meta.yml | 2 +- tools/fastq_screen/meta.yml | 6 +++--- tools/fastqc/meta.yml | 7 +++---- tools/gatk/dict/meta.yml | 6 +++--- tools/hisat2/meta.yml | 6 +++--- tools/htslib/tabix/meta.yml | 6 +++--- tools/multiqc/meta.yml | 4 ++-- tools/samtools/faidx/meta.yml | 6 +++--- tools/samtools/index/meta.yml | 6 +++--- tools/samtools/sort/meta.yml | 6 +++--- tools/shovill/meta.yml | 2 +- tools/tcoffee/meta.yml | 6 +++--- tools/trim_galore/meta.yml | 9 ++++----- tools/umi_tools/umi_tools.yml | 10 +++++----- 18 files changed, 52 insertions(+), 54 deletions(-) diff --git a/test-datasets b/test-datasets index aae85a5c..e5fef889 160000 --- a/test-datasets +++ b/test-datasets @@ -1 +1 @@ -Subproject commit aae85a5c9c72238959108212481ce83bae569709 +Subproject commit e5fef88994b8d34c7bf4b07116e5f7a330d2ee3b diff --git a/tools/bowtie2/meta.yml b/tools/bowtie2/meta.yml index f30ee823..e742b1d0 100644 --- a/tools/bowtie2/meta.yml +++ b/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" diff --git a/tools/bwa/index/meta.yml b/tools/bwa/index/meta.yml index d03c71a2..49fa3c44 100644 --- a/tools/bwa/index/meta.yml +++ b/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" diff --git a/tools/bwa/mem/meta.yml b/tools/bwa/mem/meta.yml index 2ea48a28..d8ae9a7d 100644 --- a/tools/bwa/mem/meta.yml +++ b/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" diff --git a/tools/cutadapt/meta.yml b/tools/cutadapt/meta.yml index bb3bb8a8..eee43a07 100644 --- a/tools/cutadapt/meta.yml +++ b/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" diff --git a/tools/fastq_screen/meta.yml b/tools/fastq_screen/meta.yml index 4b4e56bd..8ec1348e 100644 --- a/tools/fastq_screen/meta.yml +++ b/tools/fastq_screen/meta.yml @@ -25,7 +25,7 @@ output: - report: type: file description: FastQ Screen report - pattern: *_screen.{txt,html,png} - optional_pattern: *_screen.bisulfite_orientation.png + pattern: "*_screen.{txt,html,png}" + optional_pattern: "*_screen.bisulfite_orientation.png" authors: - - @FelixKrueger + - "@FelixKrueger" diff --git a/tools/fastqc/meta.yml b/tools/fastqc/meta.yml index bfe0f6cf..113ca464 100644 --- a/tools/fastqc/meta.yml +++ b/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 - - @FelixKrueger + - "@ewels" + - "@FelixKrueger" diff --git a/tools/gatk/dict/meta.yml b/tools/gatk/dict/meta.yml index 527d6a69..e03282bb 100644 --- a/tools/gatk/dict/meta.yml +++ b/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" diff --git a/tools/hisat2/meta.yml b/tools/hisat2/meta.yml index d5f5e403..811727a7 100644 --- a/tools/hisat2/meta.yml +++ b/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" diff --git a/tools/htslib/tabix/meta.yml b/tools/htslib/tabix/meta.yml index d35ec2f2..b8261b92 100644 --- a/tools/htslib/tabix/meta.yml +++ b/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" diff --git a/tools/multiqc/meta.yml b/tools/multiqc/meta.yml index 04e9ca42..86a9799b 100644 --- a/tools/multiqc/meta.yml +++ b/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" diff --git a/tools/samtools/faidx/meta.yml b/tools/samtools/faidx/meta.yml index 777eb051..95c2bf4b 100644 --- a/tools/samtools/faidx/meta.yml +++ b/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" diff --git a/tools/samtools/index/meta.yml b/tools/samtools/index/meta.yml index e665789b..35d34802 100644 --- a/tools/samtools/index/meta.yml +++ b/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" diff --git a/tools/samtools/sort/meta.yml b/tools/samtools/sort/meta.yml index 60f9e96b..1e042f0d 100644 --- a/tools/samtools/sort/meta.yml +++ b/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" diff --git a/tools/shovill/meta.yml b/tools/shovill/meta.yml index 7c204c24..f955fa59 100644 --- a/tools/shovill/meta.yml +++ b/tools/shovill/meta.yml @@ -27,4 +27,4 @@ output: description: fasta file pattern: ${sample_id}.fasta authors: - - @annacprice + - "@annacprice" diff --git a/tools/tcoffee/meta.yml b/tools/tcoffee/meta.yml index e15c2e12..1e4a49eb 100644 --- a/tools/tcoffee/meta.yml +++ b/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" diff --git a/tools/trim_galore/meta.yml b/tools/trim_galore/meta.yml index b3d42f81..642fb51b 100644 --- a/tools/trim_galore/meta.yml +++ b/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 - - @FelixKrueger + - "@ewels" + - "@FelixKrueger" diff --git a/tools/umi_tools/umi_tools.yml b/tools/umi_tools/umi_tools.yml index b04f0f4e..fcc53b46 100644 --- a/tools/umi_tools/umi_tools.yml +++ b/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 - - @chris-cheshire + - "@candiceh08" + - "@chris-cheshire"