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Fix YAML validation errors

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This commit is contained in:
Phil Ewels 2020-07-11 13:54:12 +02:00
parent 263f48d520
commit 47d55001fa
18 changed files with 52 additions and 54 deletions
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2
test-datasets

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

6
tools/bowtie2/meta.yml
View file

@ -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"

6
tools/bwa/index/meta.yml
View file

@ -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"

10
tools/bwa/mem/meta.yml
View file

@ -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"

2
tools/cutadapt/meta.yml
View file

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

6
tools/fastq_screen/meta.yml
View file

@ -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"

7
tools/fastqc/meta.yml
View file

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

6
tools/gatk/dict/meta.yml
View file

@ -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"

6
tools/hisat2/meta.yml
View file

@ -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"

6
tools/htslib/tabix/meta.yml
View file

@ -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"

4
tools/multiqc/meta.yml
View file

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

6
tools/samtools/faidx/meta.yml
View file

@ -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"

6
tools/samtools/index/meta.yml
View file

@ -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"

6
tools/samtools/sort/meta.yml
View file

@ -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"

2
tools/shovill/meta.yml
View file

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

6
tools/tcoffee/meta.yml
View file

@ -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"

9
tools/trim_galore/meta.yml
View file

@ -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"

10
tools/umi_tools/umi_tools.yml
View file

@ -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"