From 7ab8c61ede2a40c165927857e2a5e1a7601cf43f Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Mon, 14 Aug 2023 16:45:47 -0400 Subject: [PATCH 1/4] Unhide params trim_fastq, umi_read_structure, and aligner. Signed-off-by: Rob Syme --- nextflow_schema.json | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 8d96f33d61..36c92585ad 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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) " }, "clip_r1": { "type": "integer", @@ -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": { @@ -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" }, "save_mapped": { "type": "boolean", From b0d124891ea70de13054c52478643fefd71c3da7 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Mon, 14 Aug 2023 21:31:15 -0400 Subject: [PATCH 2/4] Update nextflow_schema.json While here, remove backticks from Sarek and DragMap software names. Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 36c92585ad..2fbbcc79de 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -212,7 +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" + "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" }, "save_mapped": { "type": "boolean", From cbe8ccd36e137ea4e62c0ae28a4c910c48b9eea5 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Tue, 15 Aug 2023 06:57:49 -0400 Subject: [PATCH 3/4] Update nextflow_schema.json Co-authored-by: Maxime U Garcia --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 2fbbcc79de..f3605f6313 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -212,7 +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" + "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`. For more info see [here](https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode)." }, "save_mapped": { "type": "boolean", From 6a840e7cb824eed5c96ee29a2fde2cb21db99ecd Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Tue, 15 Aug 2023 06:58:02 -0400 Subject: [PATCH 4/4] Update nextflow_schema.json Co-authored-by: Maxime U Garcia --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index f3605f6313..01181b7ec3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -130,7 +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) " + "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)." }, "clip_r1": { "type": "integer",