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Update nextflow_schema.json

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Thomas Rich 2022-07-27 14:35:40 +00:00 committed by Neil Horner
parent 23c2e96939
commit 7a61c04ed9
3 changed files with 4 additions and 1 deletions
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2
.gitlab-ci.yml
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@ -9,4 +9,4 @@ variables:
# Only common file inputs and option values need to be given here # Only common file inputs and option values need to be given here
# (not things such as -profile) # (not things such as -profile)
NF_WORKFLOW_OPTS: "--fastq test_data/fastq \ NF_WORKFLOW_OPTS: "--fastq test_data/fastq \
--ref_genome test_data/SIRV_150601a.fasta --ref_annotation test_data/SIRV_isofroms.gtf" --ref_genome test_data/SIRV_150601a.fasta --ref_annotation test_data/SIRV_isoforms.gtf"

3
nextflow_schema.json
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@ -21,6 +21,7 @@
"fastq": { "fastq": {
"type": "string", "type": "string",
"format": "path", "format": "path",
"demo_data": "${projectDir}/test_data/fastq",
"description": "A fastq file or directory containing fastq input files or directories of input files.", "description": "A fastq file or directory containing fastq input files or directories of input files.",
"help_text": "If directories named \\\"barcode*\\\" are found under the `--fastq` directory the data is assumed to be multiplex and each barcode directory will be processed independently. If `.fastq(.gz)` files are found under the `--fastq` directory the sample is assumed to not be multiplexed. In this second case `--samples` should be a simple name rather than a CSV file." "help_text": "If directories named \\\"barcode*\\\" are found under the `--fastq` directory the data is assumed to be multiplex and each barcode directory will be processed independently. If `.fastq(.gz)` files are found under the `--fastq` directory the sample is assumed to not be multiplexed. In this second case `--samples` should be a simple name rather than a CSV file."
}, },
@ -41,11 +42,13 @@
"ref_genome": { "ref_genome": {
"type": "string", "type": "string",
"format": "file-path", "format": "file-path",
"demo_data": "${projectDir}/test_data/SIRV_150601a.fasta",
"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow" "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow"
}, },
"ref_annotation": { "ref_annotation": {
"type": "string", "type": "string",
"format": "file-path", "format": "file-path",
"demo_data": "${projectDir}/test_data/SIRV_isoforms.gtf",
"description": "A reference annotation of gff format" "description": "A reference annotation of gff format"
} }
}, },

0
test_data/SIRV_isofroms.gtf → test_data/SIRV_isoforms.gtf
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