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Get release ready #49

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merged 2 commits into from
May 3, 2023
Merged

Get release ready #49

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527f7fd
get release ready
SusiJo May 3, 2023
8fa9f38
rm line
SusiJo May 3, 2023
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7 changes: 0 additions & 7 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1 @@
repository_type: pipeline
lint:
files_exist:
- conf/igenomes.config
files_unchanged:
- .github/workflows/branch.yml
- lib/NfcoreSchema.groovy
template_strings: False
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -232,7 +232,7 @@ manifest {
description = """Workflow converts one or multiple bam/cram files to fastq format"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
version = '2.0.0dev'
version = '2.0'
doi = ''
}

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15 changes: 10 additions & 5 deletions nextflow_schema.json
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Expand Up @@ -39,24 +39,29 @@
"chr": {
"type": "string",
"default": "None",
"fa_icon": "fas fa-clock"
"fa_icon": "fas fa-clock",
"description": "Only use reads mapping to a specific chromosome/region. Has to be specified as in bam: i.e chr1, chr{1..22} (gets all reads mapping to chr1 to 22), 1, \"X Y\", incorrect naming will lead to a potentially silent error."
},
"no_read_QC": {
"type": "boolean",
"fa_icon": "fas fa-clock"
"fa_icon": "fas fa-clock",
"description": "If specified, no quality control will be performed on extracted reads. Useful, if this is done anyways in the subsequent workflow."
},
"no_stats": {
"type": "boolean",
"fa_icon": "fas fa-clock"
"fa_icon": "fas fa-clock",
"description": "If specified, skips all quality control and stats computation, including `FastQC` on both input bam and output reads, `samtools flagstat`, `samtools idxstats`, and `samtools stats`."
},
"reads_in_memory": {
"type": "integer",
"default": 100000,
"fa_icon": "fas fa-clock"
"fa_icon": "fas fa-clock",
"description": "Reads to store in memory [default = '100000']. Only relevant for use with `--samtools_collate_fast`."
},
"samtools_collate_fast": {
"type": "boolean",
"fa_icon": "fas fa-clock"
"fa_icon": "fas fa-clock",
"description": "Uses fast mode for samtools collate in `sortExtractMapped`, `sortExtractUnmapped` and `sortExtractSingleEnd`."
}
}
},
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