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Unhide params trim_fastq, umi_read_structure, and aligner. #1179

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merged 4 commits into from
Aug 15, 2023
Merged

Unhide params trim_fastq, umi_read_structure, and aligner. #1179

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7ab8c61
Unhide params trim_fastq, umi_read_structure, and aligner.
robsyme Aug 14, 2023
b0d1248
Update nextflow_schema.json
robsyme Aug 15, 2023
cbe8ccd
Update nextflow_schema.json
robsyme Aug 15, 2023
6a840e7
Update nextflow_schema.json
robsyme Aug 15, 2023
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7 changes: 2 additions & 5 deletions nextflow_schema.json
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Expand Up @@ -130,8 +130,7 @@
"type": "boolean",
"fa_icon": "fas fa-cut",
"description": "Run FastP for read trimming",
"help_text": "Use this to perform adapter trimming. Adapter are detected automatically by using the FastP flag `--detect_adapter_for_pe`. For more info see [FastP](https://github.com/OpenGene/fastp) ",
"hidden": true
"help_text": "Use this to perform adapter trimming. Adapter are detected automatically by using the FastP flag `--detect_adapter_for_pe`. For more info see [FastP](https://github.com/OpenGene/fastp) "
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},
"clip_r1": {
"type": "integer",
Expand Down Expand Up @@ -183,7 +182,6 @@
"type": "string",
"fa_icon": "fas fa-tape",
"description": "Specify UMI read structure",
"hidden": true,
"help_text": "One structure if UMI is present on one end (i.e. '+T 2M11S+T'), or two structures separated by a blank space if UMIs a present on both ends (i.e. '2M11S+T 2M11S+T'); please note, this does not handle duplex-UMIs.\n\nFor more info on UMI usage in the pipeline, also check docs [here](./docs/usage.md/#how-to-handle-umis)."
},
"group_by_umi_strategy": {
Expand Down Expand Up @@ -214,8 +212,7 @@
"fa_icon": "fas fa-puzzle-piece",
"enum": ["bwa-mem", "bwa-mem2", "dragmap", "sentieon-bwamem"],
"description": "Specify aligner to be used to map reads to reference genome.",
"help_text": "`Sarek` will build missing indices automatically if not provided. Set `--bwa false` if indices should be (re-)built.\nIf `DragMap` is selected as aligner, it is recommended to skip baserecalibration with `--skip_tools baserecalibrator`. See [here](https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode) for more info.\n",
"hidden": true
"help_text": "`Sarek` will build missing indices automatically if not provided. Set `--bwa false` if indices should be (re-)built.\nIf `DragMap` is selected as aligner, it is recommended to skip baserecalibration with `--skip_tools baserecalibrator`. See [here](https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode) for more info.\n"
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},
"save_mapped": {
"type": "boolean",
Expand Down