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fixed prettier
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@daisymut
daisymut committed Nov 18, 2024
1 parent 3ed6734 commit d529170
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Showing 3 changed files with 31 additions and 92 deletions.
8 changes: 4 additions & 4 deletions assets/schema_input.json
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,10 @@
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"experimentalID": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "experimentalID must be provided and cannot contain spaces",
"meta": ["id"]
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "experimentalID must be provided and cannot contain spaces",
"meta": ["id"]
},
"fraction": {
"type": "string",
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101 changes: 25 additions & 76 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,131 +8,92 @@
"bwa/aln": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fastq_align_bwaaln",
"modules"
]
"installed_by": ["fastq_align_bwaaln", "modules"]
},
"bwa/index": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"bwa/sampe": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fastq_align_bwaaln"
]
"installed_by": ["fastq_align_bwaaln"]
},
"bwa/samse": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"fastq_align_bwaaln"
]
"installed_by": ["fastq_align_bwaaln"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"deeptools/bamcoverage": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": [
"bam_markduplicates_picard",
"modules"
]
"installed_by": ["bam_markduplicates_picard", "modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"bam_stats_samtools"
]
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"bam_stats_samtools"
]
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"bam_markduplicates_picard",
"fastq_align_bwaaln"
]
"installed_by": ["bam_markduplicates_picard", "fastq_align_bwaaln"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"bam_stats_samtools"
]
"installed_by": ["bam_stats_samtools"]
},
"trimgalore": {
"branch": "master",
"git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"trimmomatic": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
}
}
},
Expand All @@ -141,47 +102,35 @@
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"installed_by": [
"bam_markduplicates_picard"
]
"installed_by": ["bam_markduplicates_picard"]
},
"fastq_align_bwaaln": {
"branch": "master",
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
}
}
}
}
}
}
}
14 changes: 2 additions & 12 deletions nextflow_schema.json
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Expand Up @@ -10,10 +10,7 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"input",
"outdir"
],
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
Expand Down Expand Up @@ -179,14 +176,7 @@
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
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